3-164882802-T-C

Variant names:

• chr3-164882802-T-C
• rs1993522

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 0.28 in 151,906 control chromosomes in the GnomAD database, including 7,743 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 0.28 (7743 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 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: 0.280 AC: 42482 AN: 151788 Hom.: 7728 Cov.: 32

Gnomad AFR AF: 0.0675

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.280 AC: 42502 AN: 151906 Hom.: 7743 Cov.: 32 AF XY: 0.287 AC XY: 21330 AN XY: 74196

Gnomad4 AFR AF: 0.0673

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.326

Gnomad4 EAS AF: 0.677

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.298

Alfa AF: 0.320 Hom.: 10812

Bravo AF: 0.277

Asia WGS AF: 0.488 AC: 1693 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1993522; hg19: chr3-164600590;