3-183176548-C-T

Variant names:

• chr3-183176548-C-T
• rs512071

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 0.619 in 152,108 control chromosomes in the GnomAD database, including 31,520 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 0.62 (31520 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.748 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94131 AN: 151990 Hom.: 31527 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.619 AC: 94137 AN: 152108 Hom.: 31520 Cov.: 32 AF XY: 0.619 AC XY: 46016 AN XY: 74384

African (AFR) AF: 0.364 AC: 15090 AN: 41480

American (AMR) AF: 0.538 AC: 8226 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2777 AN: 3472

East Asian (EAS) AF: 0.578 AC: 2979 AN: 5154

South Asian (SAS) AF: 0.710 AC: 3422 AN: 4818

European-Finnish (FIN) AF: 0.765 AC: 8100 AN: 10592

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.753 AC: 51225 AN: 68000

Other (OTH) AF: 0.652 AC: 1375 AN: 2108

Alfa AF: 0.701 Hom.: 117301

Bravo AF: 0.588

Asia WGS AF: 0.605 AC: 2103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.55
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs512071; hg19: chr3-182894336;