rs3912607

Variant names:

• chr3-162780970-C-T
• rs3912607

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 0.439 in 151,290 control chromosomes in the GnomAD database, including 14,878 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 0.44 (14878 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.496 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: 0.439 AC: 66390 AN: 151172 Hom.: 14868 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.438

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.439 AC: 66429 AN: 151290 Hom.: 14878 Cov.: 31 AF XY: 0.444 AC XY: 32849 AN XY: 73934

African (AFR) AF: 0.446 AC: 18434 AN: 41302

American (AMR) AF: 0.423 AC: 6412 AN: 15142

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1390 AN: 3460

East Asian (EAS) AF: 0.110 AC: 560 AN: 5106

South Asian (SAS) AF: 0.513 AC: 2472 AN: 4816

European-Finnish (FIN) AF: 0.577 AC: 6096 AN: 10570

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.438 AC: 29628 AN: 67590

Other (OTH) AF: 0.413 AC: 866 AN: 2098

Alfa AF: 0.442 Hom.: 7352

Bravo AF: 0.425

Asia WGS AF: 0.287 AC: 998 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.31
DANN	Benign	0.23
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs3912607; hg19: chr3-162498758;