3-21339185-C-T

Variant names:

• chr3-21339185-C-T
• rs2731943

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 0.357 in 151,804 control chromosomes in the GnomAD database, including 11,472 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 0.36 (11472 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 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: 0.357 AC: 54107 AN: 151688 Hom.: 11445 Cov.: 32

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.357 AC: 54195 AN: 151804 Hom.: 11472 Cov.: 32 AF XY: 0.362 AC XY: 26834 AN XY: 74174

African (AFR) AF: 0.553 AC: 22902 AN: 41410

American (AMR) AF: 0.497 AC: 7576 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3466

East Asian (EAS) AF: 0.374 AC: 1928 AN: 5154

South Asian (SAS) AF: 0.404 AC: 1948 AN: 4818

European-Finnish (FIN) AF: 0.261 AC: 2741 AN: 10490

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.227 AC: 15436 AN: 67902

Other (OTH) AF: 0.337 AC: 710 AN: 2108

Alfa AF: 0.274 Hom.: 19722

Bravo AF: 0.381

Asia WGS AF: 0.402 AC: 1396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.43
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs2731943; hg19: chr3-21380677;