3-32183834-C-T

Variant names:

• chr3-32183834-C-T
• rs7644491

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 0.491 in 152,036 control chromosomes in the GnomAD database, including 19,597 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 0.49 (19597 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0790
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.661 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: 0.491 AC: 74554 AN: 151918 Hom.: 19584 Cov.: 32

Gnomad AFR AF: 0.668

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.597

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.491 AC: 74603 AN: 152036 Hom.: 19597 Cov.: 32 AF XY: 0.497 AC XY: 36966 AN XY: 74320

African (AFR) AF: 0.668 AC: 27674 AN: 41456

American (AMR) AF: 0.398 AC: 6078 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1219 AN: 3472

East Asian (EAS) AF: 0.607 AC: 3137 AN: 5170

South Asian (SAS) AF: 0.596 AC: 2878 AN: 4826

European-Finnish (FIN) AF: 0.554 AC: 5844 AN: 10552

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26359 AN: 67978

Other (OTH) AF: 0.464 AC: 978 AN: 2106

Alfa AF: 0.420 Hom.: 41609

Bravo AF: 0.488

Asia WGS AF: 0.602 AC: 2093 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.8
DANN	Benign	0.79
PhyloP100		0.079

Splicing

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

Other links and lift over

dbSNP: rs7644491; hg19: chr3-32225326; COSMIC: COSV53458427;