rs3892715

Variant names:

• chr3-195037281-C-T
• rs3892715

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 0.518 in 151,950 control chromosomes in the GnomAD database, including 21,220 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 0.52 (21220 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.276
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.659 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: 0.518 AC: 78605 AN: 151832 Hom.: 21185 Cov.: 31

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.518 AC: 78688 AN: 151950 Hom.: 21220 Cov.: 31 AF XY: 0.510 AC XY: 37827 AN XY: 74216

African (AFR) AF: 0.666 AC: 27612 AN: 41464

American (AMR) AF: 0.458 AC: 6988 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1589 AN: 3472

East Asian (EAS) AF: 0.318 AC: 1640 AN: 5162

South Asian (SAS) AF: 0.408 AC: 1963 AN: 4810

European-Finnish (FIN) AF: 0.429 AC: 4514 AN: 10516

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32740 AN: 67942

Other (OTH) AF: 0.494 AC: 1041 AN: 2106

Alfa AF: 0.494 Hom.: 50486

Bravo AF: 0.530

Asia WGS AF: 0.390 AC: 1357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.022
DANN	Benign	0.48
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs3892715; hg19: chr3-194758010;