3-164882802-T-C

Position:

• chr3-164882802-T-C

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.167

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.164882802T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;