chr3-186833893-T-C

Variant names:

• chr3-186833893-T-C
• rs4632532

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 0.43 in 151,338 control chromosomes in the GnomAD database, including 14,928 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 0.43 (14928 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285

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 (AFR) allele frequency at 95% confidence interval = 0.537 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: 0.430 AC: 65056 AN: 151220 Hom.: 14909 Cov.: 29

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.430 AC: 65122 AN: 151338 Hom.: 14928 Cov.: 29 AF XY: 0.441 AC XY: 32569 AN XY: 73914

Gnomad4 AFR AF: 0.543

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.353

Gnomad4 EAS AF: 0.483

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.377

Alfa AF: 0.402 Hom.: 1616

Bravo AF: 0.423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4632532; hg19: chr3-186551682;