3-167963062-G-A

Position:

• chr3-167963062-G-A

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 0.239 in 151,784 control chromosomes in the GnomAD database, including 5,039 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 0.24 (5039 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36281 AN: 151664 Hom.: 5040 Cov.: 31

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.0457

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.239 AC: 36291 AN: 151784 Hom.: 5039 Cov.: 31 AF XY: 0.235 AC XY: 17442 AN XY: 74164

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.0460

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.249

Alfa AF: 0.298 Hom.: 5977

Bravo AF: 0.226

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13069589; hg19: chr3-167680850;