Name: rs756236348
Published: September 21, 2022
License: Open Access

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs756236348

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:136671026-136671028 (GRCh38.p14) Help
The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.
Alleles: delTG / dupTG
Variation Type: Indel Insertion and Deletion
Frequency: delTG=0.00194 (31/15976, 14KJPN)
delTG=0.00034 (4/11862, ALFA)
delTG=0.0014 (10/7256, 8.3KJPN) (+ 1 more)
dupTG=0.000 (0/182, ExAC)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: EGFL7 : Intron Variant
MIR126 : 500B Downstream Variant
Publications: 0 citations
Genomic View: See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	HTRZ	HWEP
Total	Global	11862	GTG=0.99966	G=0.00034	0.999326	0.000674	0
European	Sub	7618	GTG=0.9999	G=0.0001	0.999737	0.000263	0
African	Sub	2816	GTG=0.9989	G=0.0011	0.997869	0.002131	0
African Others	Sub	108	GTG=0.991	G=0.009	0.981481	0.018519	0
African American	Sub	2708	GTG=0.9993	G=0.0007	0.998523	0.001477	0
Asian	Sub	108	GTG=1.000	G=0.000	1.0	0.0	N/A
East Asian	Sub	84	GTG=1.00	G=0.00	1.0	0.0	N/A
Other Asian	Sub	24	GTG=1.00	G=0.00	1.0	0.0	N/A
Latin American 1	Sub	146	GTG=1.000	G=0.000	1.0	0.0	N/A
Latin American 2	Sub	610	GTG=1.000	G=0.000	1.0	0.0	N/A
South Asian	Sub	94	GTG=1.00	G=0.00	1.0	0.0	N/A
Other	Sub	470	GTG=1.000	G=0.000	1.0	0.0	N/A

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
14KJPN	JAPANESE	Study-wide	15976	GTG=0.99806	delTG=0.00194
Allele Frequency Aggregator	Total	Global	11862	GTG=0.99966	delTG=0.00034
Allele Frequency Aggregator	European	Sub	7618	GTG=0.9999	delTG=0.0001
Allele Frequency Aggregator	African	Sub	2816	GTG=0.9989	delTG=0.0011
Allele Frequency Aggregator	Latin American 2	Sub	610	GTG=1.000	delTG=0.000
Allele Frequency Aggregator	Other	Sub	470	GTG=1.000	delTG=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	GTG=1.000	delTG=0.000
Allele Frequency Aggregator	Asian	Sub	108	GTG=1.000	delTG=0.000
Allele Frequency Aggregator	South Asian	Sub	94	GTG=1.00	delTG=0.00
8.3KJPN	JAPANESE	Study-wide	7256	GTG=0.9986	delTG=0.0014
ExAC	Global	Study-wide	182	- No frequency provided	dupTG=0.000
ExAC	Europe	Sub	80	- No frequency provided	dupTG=0.00
ExAC	Asian	Sub	54	- No frequency provided	dupTG=0.00
ExAC	African	Sub	38	- No frequency provided	dupTG=0.00
ExAC	American	Sub	6	- No frequency provided	dupTG=0.0
ExAC	Other	Sub	4	- No frequency provided	dupTG=0.0

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements

Sequence name	Change
GRCh38.p14 chr 9	NC_000009.12:g.136671027_136671028del
GRCh38.p14 chr 9	NC_000009.12:g.136671027_136671028dup
GRCh37.p13 chr 9	NC_000009.11:g.139565479_139565480del
GRCh37.p13 chr 9	NC_000009.11:g.139565479_139565480dup

Gene: EGFL7, EGF like domain multiple 7 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EGFL7 transcript variant 1	NM_016215.5:c.636+13_636+… NM_016215.5:c.636+13_636+14del	N/A	Intron Variant
EGFL7 transcript variant 2	NM_201446.3:c.636+13_636+… NM_201446.3:c.636+13_636+14del	N/A	Intron Variant
EGFL7 transcript variant 3	NR_045110.2:n.	N/A	Intron Variant
EGFL7 transcript variant 4	NR_045111.2:n.	N/A	Intron Variant
EGFL7 transcript variant 5	NR_046367.1:n.	N/A	Intron Variant
EGFL7 transcript variant X5	XM_006717141.4:c.474+13_4… XM_006717141.4:c.474+13_474+14del	N/A	Intron Variant
EGFL7 transcript variant X8	XM_011518767.1:c.462+13_4… XM_011518767.1:c.462+13_462+14del	N/A	Intron Variant
EGFL7 transcript variant X9	XM_011518768.1:c.462+13_4… XM_011518768.1:c.462+13_462+14del	N/A	Intron Variant
EGFL7 transcript variant X2	XM_017014795.1:c.564+13_5… XM_017014795.1:c.564+13_564+14del	N/A	Intron Variant
EGFL7 transcript variant X3	XM_017014796.1:c.561+13_5… XM_017014796.1:c.561+13_561+14del	N/A	Intron Variant
EGFL7 transcript variant X6	XM_017014798.1:c.462+13_4… XM_017014798.1:c.462+13_462+14del	N/A	Intron Variant
EGFL7 transcript variant X7	XM_017014799.1:c.462+13_4… XM_017014799.1:c.462+13_462+14del	N/A	Intron Variant
EGFL7 transcript variant X1	XM_047423451.1:c.636+13_6… XM_047423451.1:c.636+13_636+14del	N/A	Intron Variant
EGFL7 transcript variant X4	XM_047423452.1:c.474+13_4… XM_047423452.1:c.474+13_474+14del	N/A	Intron Variant
EGFL7 transcript variant X10	XM_047423453.1:c.402+13_4… XM_047423453.1:c.402+13_402+14del	N/A	Intron Variant

Gene: MIR126, microRNA 126 (plus strand) : 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
MIR126 transcript	NR_029695.1:n.	N/A	Downstream Transcript Variant

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement	GTG=	delTG	dupTG
GRCh38.p14 chr 9	NC_000009.12:g.136671026_136671028=	NC_000009.12:g.136671027_136671028del	NC_000009.12:g.136671027_136671028dup
GRCh37.p13 chr 9	NC_000009.11:g.139565478_139565480=	NC_000009.11:g.139565479_139565480del	NC_000009.11:g.139565479_139565480dup
EGFL7 transcript variant 1	NM_016215.4:c.636+12=	NM_016215.4:c.636+13_636+14del	NM_016215.4:c.636+13_636+14dup
EGFL7 transcript variant 1	NM_016215.5:c.636+12=	NM_016215.5:c.636+13_636+14del	NM_016215.5:c.636+13_636+14dup
EGFL7 transcript variant 2	NM_201446.2:c.636+12=	NM_201446.2:c.636+13_636+14del	NM_201446.2:c.636+13_636+14dup
EGFL7 transcript variant 2	NM_201446.3:c.636+12=	NM_201446.3:c.636+13_636+14del	NM_201446.3:c.636+13_636+14dup
EGFL7 transcript variant X5	XM_006717141.4:c.474+12=	XM_006717141.4:c.474+13_474+14del	XM_006717141.4:c.474+13_474+14dup
EGFL7 transcript variant X8	XM_011518767.1:c.462+12=	XM_011518767.1:c.462+13_462+14del	XM_011518767.1:c.462+13_462+14dup
EGFL7 transcript variant X9	XM_011518768.1:c.462+12=	XM_011518768.1:c.462+13_462+14del	XM_011518768.1:c.462+13_462+14dup
EGFL7 transcript variant X2	XM_017014795.1:c.564+12=	XM_017014795.1:c.564+13_564+14del	XM_017014795.1:c.564+13_564+14dup
EGFL7 transcript variant X3	XM_017014796.1:c.561+12=	XM_017014796.1:c.561+13_561+14del	XM_017014796.1:c.561+13_561+14dup
EGFL7 transcript variant X6	XM_017014798.1:c.462+12=	XM_017014798.1:c.462+13_462+14del	XM_017014798.1:c.462+13_462+14dup
EGFL7 transcript variant X7	XM_017014799.1:c.462+12=	XM_017014799.1:c.462+13_462+14del	XM_017014799.1:c.462+13_462+14dup
EGFL7 transcript variant X1	XM_047423451.1:c.636+12=	XM_047423451.1:c.636+13_636+14del	XM_047423451.1:c.636+13_636+14dup
EGFL7 transcript variant X4	XM_047423452.1:c.474+12=	XM_047423452.1:c.474+13_474+14del	XM_047423452.1:c.474+13_474+14dup
EGFL7 transcript variant X10	XM_047423453.1:c.402+12=	XM_047423453.1:c.402+13_402+14del	XM_047423453.1:c.402+13_402+14dup

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

5 SubSNP, 4 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EVA_EXAC	ss1711927004	Apr 01, 2015 (144)
2	TMC_SNPDB	ss1997225354	Jan 10, 2018 (151)
3	EVA_DECODE	ss3724962703	Jul 13, 2019 (153)
4	TOMMO_GENOMICS	ss5195775124	Apr 26, 2021 (155)
5	TOMMO_GENOMICS	ss5740472504	Oct 13, 2022 (156)
6	ExAC	NC_000009.11 - 139565478	Oct 12, 2018 (152)
7	8.3KJPN	NC_000009.11 - 139565478	Apr 26, 2021 (155)
8	14KJPN	NC_000009.12 - 136671026	Oct 13, 2022 (156)
9	ALFA	NC_000009.12 - 136671026	Apr 26, 2021 (155)

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
53744431, ss1997225354, ss5195775124	NC_000009.11:139565477:GT:	NC_000009.12:136671025:GTG:G	(self)
74309608, ss3724962703, ss5740472504	NC_000009.12:136671025:GT:	NC_000009.12:136671025:GTG:G	(self)
11968344330	NC_000009.12:136671025:GTG:G	NC_000009.12:136671025:GTG:G	(self)
9897611, ss1711927004	NC_000009.11:139565477::GT	NC_000009.12:136671025:GTG:GTGTG	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs756236348

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:

Select flank length:

Genomic regions, transcripts, and products
Top▲ Help
NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs756236348