7-131676169-A-C

Variant names:

• chr7-131676169-A-C
• rs11765576

Variant summary

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

The variant allele was found at a frequency of 0.476 in 152,116 control chromosomes in the GnomAD database, including 19,835 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 0.48 (19835 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

 

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

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72363 AN: 151998 Hom.: 19828 Cov.: 33

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.775

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.476 AC: 72377 AN: 152116 Hom.: 19835 Cov.: 33 AF XY: 0.477 AC XY: 35480 AN XY: 74338

African (AFR) AF: 0.209 AC: 8680 AN: 41500

American (AMR) AF: 0.422 AC: 6453 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2394 AN: 3468

East Asian (EAS) AF: 0.384 AC: 1987 AN: 5168

South Asian (SAS) AF: 0.604 AC: 2912 AN: 4820

European-Finnish (FIN) AF: 0.629 AC: 6654 AN: 10576

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.608 AC: 41332 AN: 67978

Other (OTH) AF: 0.508 AC: 1074 AN: 2116

Alfa AF: 0.566 Hom.: 107327

Bravo AF: 0.446

Asia WGS AF: 0.483 AC: 1678 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.064
DANN	Benign	0.62
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs11765576; hg19: chr7-131360928;