chr3-148694621-A-C

Variant names:

• chr3-148694621-A-C
• rs4681157

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 0.498 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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.160 AC: 6594 AN: 41292

American (AMR) AF: 0.660 AC: 10064 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1913 AN: 3468

East Asian (EAS) AF: 0.811 AC: 4186 AN: 5160

South Asian (SAS) AF: 0.546 AC: 2628 AN: 4812

European-Finnish (FIN) AF: 0.679 AC: 7161 AN: 10546

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41400 AN: 67900

Other (OTH) AF: 0.510 AC: 1073 AN: 2104

Alfa AF: 0.386 Hom.: 1296

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs4681157; hg19: chr3-148412408;