chr11-11760618-G-A

Variant names:

• chr11-11760618-G-A
• rs7937815
• ENST00000794530.1:n.431-26977C>T

Variant summary

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

The ENST00000794530.1(ENSG00000286959):​n.431-26977C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.524 in 151,788 control chromosomes in the GnomAD database, including 21,051 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 0.52 (21051 hom., cov: 31)
• Consequence: ENSG00000286959 ENST00000794530.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 0 publications found

Genes affected

ENSG00000286959 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794530.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286959	ENST00000794530.1		n.431-26977C>T		intron	N/A
	ENSG00000286959	ENST00000794531.1		n.65-26977C>T		intron	N/A
	ENSG00000286959	ENST00000794532.1		n.142-26977C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79509 AN: 151670 Hom.: 21023 Cov.: 31

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.524 AC: 79586 AN: 151788 Hom.: 21051 Cov.: 31 AF XY: 0.529 AC XY: 39245 AN XY: 74136

African (AFR) AF: 0.456 AC: 18870 AN: 41362

American (AMR) AF: 0.630 AC: 9614 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2209 AN: 3470

East Asian (EAS) AF: 0.654 AC: 3368 AN: 5148

South Asian (SAS) AF: 0.664 AC: 3197 AN: 4814

European-Finnish (FIN) AF: 0.476 AC: 5005 AN: 10504

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35538 AN: 67922

Other (OTH) AF: 0.551 AC: 1160 AN: 2106

Alfa AF: 0.512 Hom.: 2553

Bravo AF: 0.527

Asia WGS AF: 0.644 AC: 2241 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.9
DANN	Benign	0.80
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs7937815; hg19: chr11-11782165;