3-186833893-T-C

Variant names:

• chr3-186833893-T-C
• rs4632532

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 0.43 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
• Publications: 18 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 (AFR) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.543 AC: 22384 AN: 41200

American (AMR) AF: 0.431 AC: 6558 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1220 AN: 3454

East Asian (EAS) AF: 0.483 AC: 2469 AN: 5116

South Asian (SAS) AF: 0.341 AC: 1631 AN: 4790

European-Finnish (FIN) AF: 0.604 AC: 6326 AN: 10478

Middle Eastern (MID) AF: 0.330 AC: 95 AN: 288

European-Non Finnish (NFE) AF: 0.341 AC: 23123 AN: 67804

Other (OTH) AF: 0.377 AC: 789 AN: 2092

Alfa AF: 0.408 Hom.: 1738

Bravo AF: 0.423

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.70
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs4632532; hg19: chr3-186551682;