3-149437531-A-G

Variant names:

• chr3-149437531-A-G
• rs2043083

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 0.798 in 152,224 control chromosomes in the GnomAD database, including 48,604 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 0.80 (48604 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.453
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.828 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: 0.798 AC: 121379 AN: 152106 Hom.: 48554 Cov.: 33

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.791

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.798 AC: 121487 AN: 152224 Hom.: 48604 Cov.: 33 AF XY: 0.797 AC XY: 59339 AN XY: 74428

African (AFR) AF: 0.815 AC: 33846 AN: 41542

American (AMR) AF: 0.841 AC: 12850 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.680 AC: 2357 AN: 3466

East Asian (EAS) AF: 0.740 AC: 3827 AN: 5174

South Asian (SAS) AF: 0.836 AC: 4033 AN: 4824

European-Finnish (FIN) AF: 0.781 AC: 8274 AN: 10594

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.791 AC: 53790 AN: 68014

Other (OTH) AF: 0.816 AC: 1727 AN: 2116

Alfa AF: 0.795 Hom.: 46107

Bravo AF: 0.800

Asia WGS AF: 0.817 AC: 2839 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.0
DANN	Benign	0.58
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs2043083; hg19: chr3-149155318;