3-87163656-A-G

Variant names:

• chr3-87163656-A-G
• rs1976324

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 0.746 in 151,862 control chromosomes in the GnomAD database, including 43,262 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 0.75 (43262 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.330
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.915 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: 0.746 AC: 113177 AN: 151744 Hom.: 43231 Cov.: 30

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.720

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.684

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.746 AC: 113255 AN: 151862 Hom.: 43262 Cov.: 30 AF XY: 0.741 AC XY: 54952 AN XY: 74164

African (AFR) AF: 0.923 AC: 38284 AN: 41492

American (AMR) AF: 0.648 AC: 9848 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.720 AC: 2497 AN: 3470

East Asian (EAS) AF: 0.741 AC: 3827 AN: 5164

South Asian (SAS) AF: 0.643 AC: 3087 AN: 4798

European-Finnish (FIN) AF: 0.644 AC: 6771 AN: 10512

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.684 AC: 46483 AN: 67912

Other (OTH) AF: 0.731 AC: 1539 AN: 2106

Alfa AF: 0.718 Hom.: 6946

Bravo AF: 0.754

Asia WGS AF: 0.689 AC: 2397 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.24
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs1976324; hg19: chr3-87212806;