chr3-148748576-G-A

Variant names:

• chr3-148748576-G-A
• rs427832

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 0.506 in 151,936 control chromosomes in the GnomAD database, including 20,399 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 0.51 (20399 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.735 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: 0.506 AC: 76851 AN: 151818 Hom.: 20383 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.506 AC: 76893 AN: 151936 Hom.: 20399 Cov.: 31 AF XY: 0.514 AC XY: 38200 AN XY: 74266

African (AFR) AF: 0.367 AC: 15190 AN: 41438

American (AMR) AF: 0.553 AC: 8436 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1589 AN: 3468

East Asian (EAS) AF: 0.755 AC: 3897 AN: 5164

South Asian (SAS) AF: 0.549 AC: 2633 AN: 4792

European-Finnish (FIN) AF: 0.679 AC: 7166 AN: 10556

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36398 AN: 67942

Other (OTH) AF: 0.511 AC: 1077 AN: 2108

Alfa AF: 0.524 Hom.: 88797

Bravo AF: 0.491

Asia WGS AF: 0.633 AC: 2199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.56
PhyloP100		0.024

Splicing

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

Other links and lift over

dbSNP: rs427832; hg19: chr3-148466363;