rs4681157

Positions:

• chr3-148694621-A-C
• chr3-148694621-A-T

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 0.498 in 151,730 control chromosomes in the GnomAD database, including 22,479 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 0.50 (22479 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75603 AN: 151614 Hom.: 22468 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.526

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.498 AC: 75621 AN: 151730 Hom.: 22479 Cov.: 32 AF XY: 0.506 AC XY: 37521 AN XY: 74150

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.811

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.510

Alfa AF: 0.232 Hom.: 401

Bravo AF: 0.488

Asia WGS AF: 0.647 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.63
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4681157; hg19: chr3-148412408;