3-172497785-C-T

Variant names:

• chr3-172497785-C-T
• rs2041693

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 0.459 in 151,962 control chromosomes in the GnomAD database, including 16,299 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 0.46 (16299 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 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: 0.459 AC: 69740 AN: 151844 Hom.: 16298 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.483

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.459 AC: 69778 AN: 151962 Hom.: 16299 Cov.: 32 AF XY: 0.456 AC XY: 33860 AN XY: 74286

African (AFR) AF: 0.529 AC: 21917 AN: 41452

American (AMR) AF: 0.374 AC: 5717 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1449 AN: 3468

East Asian (EAS) AF: 0.482 AC: 2493 AN: 5172

South Asian (SAS) AF: 0.448 AC: 2162 AN: 4822

European-Finnish (FIN) AF: 0.442 AC: 4650 AN: 10528

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.440 AC: 29886 AN: 67942

Other (OTH) AF: 0.455 AC: 962 AN: 2112

Alfa AF: 0.440 Hom.: 25514

Bravo AF: 0.457

Asia WGS AF: 0.515 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.8
DANN	Benign	0.70
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs2041693; hg19: chr3-172215575;