rs11763963

Variant names:

• chr7-26605814-T-C
• rs11763963
• ENST00000661238.2:n.980-2297A>G

Your query was ambiguous. Multiple possible variants found:

• chr7-26605814-T-C
• chr7-26605814-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661238.2(ENSG00000286507):​n.980-2297A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0575 in 152,172 control chromosomes in the GnomAD database, including 406 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.058 (406 hom., cov: 32)
• Consequence: ENSG00000286507 ENST00000661238.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 1 publications found

Genes affected

ENSG00000286507 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661238.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286507	ENST00000661238.2		n.980-2297A>G		intron	N/A
	ENSG00000286507	ENST00000719220.1		n.594-6444A>G		intron	N/A
	ENSG00000286507	ENST00000719221.1		n.481+11434A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0576 AC: 8756 AN: 152054 Hom.: 407 Cov.: 32

Gnomad AFR AF: 0.0168

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.0486

Gnomad ASJ AF: 0.0825

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0617

Gnomad OTH AF: 0.0609

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0575 AC: 8751 AN: 152172 Hom.: 406 Cov.: 32 AF XY: 0.0589 AC XY: 4381 AN XY: 74388

African (AFR) AF: 0.0168 AC: 696 AN: 41544

American (AMR) AF: 0.0485 AC: 742 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0825 AC: 286 AN: 3468

East Asian (EAS) AF: 0.245 AC: 1270 AN: 5178

South Asian (SAS) AF: 0.0861 AC: 414 AN: 4810

European-Finnish (FIN) AF: 0.0839 AC: 888 AN: 10580

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.0617 AC: 4196 AN: 67990

Other (OTH) AF: 0.0593 AC: 125 AN: 2108

Alfa AF: 0.0558 Hom.: 33

Bravo AF: 0.0536

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.93
DANN	Benign	0.57
PhyloP100		-1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11763963;

hg19: chr7-26645433;