3-143262038-T-C

Variant names:

• chr3-143262038-T-C
• rs9857832

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 0.672 in 152,094 control chromosomes in the GnomAD database, including 35,419 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 0.67 (35419 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.757 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: 0.672 AC: 102137 AN: 151976 Hom.: 35406 Cov.: 31

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.739

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.672 AC: 102174 AN: 152094 Hom.: 35419 Cov.: 31 AF XY: 0.671 AC XY: 49896 AN XY: 74352

African (AFR) AF: 0.485 AC: 20093 AN: 41464

American (AMR) AF: 0.738 AC: 11291 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.629 AC: 2184 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3019 AN: 5164

South Asian (SAS) AF: 0.710 AC: 3425 AN: 4822

European-Finnish (FIN) AF: 0.760 AC: 8033 AN: 10568

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51816 AN: 67992

Other (OTH) AF: 0.695 AC: 1468 AN: 2112

Alfa AF: 0.732 Hom.: 181663

Bravo AF: 0.661

Asia WGS AF: 0.624 AC: 2169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.61
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs9857832; hg19: chr3-142980880;