3-149437531-A-G

Variant names:

• chr3-149437531-A-G
• rs2043083

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 0.798 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.841

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.740

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.791

Gnomad4 OTH AF: 0.816

Alfa AF: 0.795 Hom.: 28886

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2043083; hg19: chr3-149155318;