rs427832

Variant names:

• chr3-148748576-G-A
• rs427832

Your query was ambiguous. Multiple possible variants found:

• chr3-148748576-G-A
• chr3-148748576-G-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 0.506 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

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 (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

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.553

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.549

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.511

Alfa AF: 0.526 Hom.: 42698

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs427832; hg19: chr3-148466363;