3-46271048-A-G

Variant names:

• chr3-46271048-A-G
• rs1027241

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 0.538 in 152,020 control chromosomes in the GnomAD database, including 22,956 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 0.54 (22956 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81721 AN: 151902 Hom.: 22927 Cov.: 31

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.566

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.909

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.538 AC: 81793 AN: 152020 Hom.: 22956 Cov.: 31 AF XY: 0.549 AC XY: 40771 AN XY: 74286

African (AFR) AF: 0.411 AC: 17036 AN: 41460

American (AMR) AF: 0.640 AC: 9780 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2024 AN: 3470

East Asian (EAS) AF: 0.909 AC: 4694 AN: 5166

South Asian (SAS) AF: 0.763 AC: 3680 AN: 4824

European-Finnish (FIN) AF: 0.547 AC: 5764 AN: 10544

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36841 AN: 67962

Other (OTH) AF: 0.588 AC: 1243 AN: 2114

Alfa AF: 0.549 Hom.: 38043

Bravo AF: 0.537

Asia WGS AF: 0.782 AC: 2714 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.6
DANN	Benign	0.78
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1027241; hg19: chr3-46312539;