3-168180033-T-C

Variant names:

• chr3-168180033-T-C
• rs2686586

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 0.38 in 151,978 control chromosomes in the GnomAD database, including 12,257 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 0.38 (12257 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.965
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.661 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: 0.380 AC: 57662 AN: 151860 Hom.: 12225 Cov.: 32

Gnomad AFR AF: 0.539

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.380 AC: 57751 AN: 151978 Hom.: 12257 Cov.: 32 AF XY: 0.382 AC XY: 28405 AN XY: 74310

African (AFR) AF: 0.540 AC: 22356 AN: 41434

American (AMR) AF: 0.382 AC: 5827 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.260 AC: 900 AN: 3466

East Asian (EAS) AF: 0.680 AC: 3521 AN: 5178

South Asian (SAS) AF: 0.474 AC: 2280 AN: 4806

European-Finnish (FIN) AF: 0.252 AC: 2667 AN: 10588

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.282 AC: 19145 AN: 67932

Other (OTH) AF: 0.329 AC: 693 AN: 2106

Alfa AF: 0.402 Hom.: 8232

Bravo AF: 0.396

Asia WGS AF: 0.542 AC: 1885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.48
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs2686586; hg19: chr3-167897821;