13-31407538-T-C

Variant names:

• chr13-31407538-T-C
• rs1359634

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 0.491 in 151,958 control chromosomes in the GnomAD database, including 19,812 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 0.49 (19812 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.377
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.774 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: 0.491 AC: 74552 AN: 151840 Hom.: 19798 Cov.: 31

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.606

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.543

Gnomad OTH AF: 0.539

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

GnomAD4 genome AF: 0.491 AC: 74590 AN: 151958 Hom.: 19812 Cov.: 31 AF XY: 0.496 AC XY: 36865 AN XY: 74262

African (AFR) AF: 0.290 AC: 12016 AN: 41458

American (AMR) AF: 0.633 AC: 9655 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.606 AC: 2103 AN: 3468

East Asian (EAS) AF: 0.794 AC: 4103 AN: 5166

South Asian (SAS) AF: 0.595 AC: 2857 AN: 4800

European-Finnish (FIN) AF: 0.481 AC: 5071 AN: 10542

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.543 AC: 36919 AN: 67944

Other (OTH) AF: 0.540 AC: 1141 AN: 2114

Alfa AF: 0.534 Hom.: 15567

Bravo AF: 0.496

Asia WGS AF: 0.646 AC: 2244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.2
DANN	Benign	0.51
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs1359634; hg19: chr13-31981675;