3-148694621-A-C

Variant names:

• chr3-148694621-A-C
• rs4681157

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;