chr3-143262038-T-C

Variant names:

• chr3-143262038-T-C
• rs9857832

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 0.672 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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.710

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.762

Gnomad4 OTH AF: 0.695

Alfa AF: 0.744 Hom.: 86911

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9857832; hg19: chr3-142980880;