chr3-87163656-A-G

Variant names:

• chr3-87163656-A-G
• rs1976324

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.923

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.720

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.644

Gnomad4 NFE AF: 0.684

Gnomad4 OTH AF: 0.731

Alfa AF: 0.712 Hom.: 6613

Bravo AF: 0.754

Asia WGS AF: 0.689 AC: 2397 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1976324; hg19: chr3-87212806;