13-31333604-C-T

Variant names:

• chr13-31333604-C-T
• rs1409379

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 0.665 in 151,888 control chromosomes in the GnomAD database, including 34,790 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 0.66 (34790 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.416
• Publications: 23 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.761 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: 0.665 AC: 100959 AN: 151770 Hom.: 34789 Cov.: 31

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.691

Gnomad ASJ AF: 0.757

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.766

Gnomad OTH AF: 0.673

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

GnomAD4 genome AF: 0.665 AC: 101002 AN: 151888 Hom.: 34790 Cov.: 31 AF XY: 0.660 AC XY: 49055 AN XY: 74270

African (AFR) AF: 0.483 AC: 19970 AN: 41356

American (AMR) AF: 0.691 AC: 10545 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.757 AC: 2627 AN: 3468

East Asian (EAS) AF: 0.572 AC: 2949 AN: 5158

South Asian (SAS) AF: 0.655 AC: 3152 AN: 4812

European-Finnish (FIN) AF: 0.685 AC: 7237 AN: 10562

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.766 AC: 52076 AN: 67948

Other (OTH) AF: 0.671 AC: 1415 AN: 2110

Alfa AF: 0.730 Hom.: 20757

Bravo AF: 0.658

Asia WGS AF: 0.625 AC: 2172 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.38
DANN	Benign	0.72
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs1409379; hg19: chr13-31907741;