3-4989276-C-T

Variant names:

• chr3-4989276-C-T
• rs2137947

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.643 in 152,048 control chromosomes in the GnomAD database, including 34,422 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 0.64 (34422 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.677

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.772 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: 0.644 AC: 97780 AN: 151928 Hom.: 34407 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.911

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.787

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.778

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.643 AC: 97821 AN: 152048 Hom.: 34422 Cov.: 32 AF XY: 0.646 AC XY: 48011 AN XY: 74334

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.660

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.787

Gnomad4 NFE AF: 0.778

Gnomad4 OTH AF: 0.676

Alfa AF: 0.750 Hom.: 57197

Bravo AF: 0.625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2137947; hg19: chr3-5030961;