13-105517653-T-C

Variant names:

• chr13-105517653-T-C
• rs1981272

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 0.402 in 152,058 control chromosomes in the GnomAD database, including 13,617 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 0.40 (13617 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61103 AN: 151940 Hom.: 13603 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.402 AC: 61141 AN: 152058 Hom.: 13617 Cov.: 32 AF XY: 0.405 AC XY: 30103 AN XY: 74344

African (AFR) AF: 0.200 AC: 8292 AN: 41514

American (AMR) AF: 0.522 AC: 7961 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1529 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2316 AN: 5152

South Asian (SAS) AF: 0.452 AC: 2179 AN: 4816

European-Finnish (FIN) AF: 0.426 AC: 4493 AN: 10558

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32906 AN: 67976

Other (OTH) AF: 0.403 AC: 849 AN: 2108

Alfa AF: 0.355 Hom.: 1624

Bravo AF: 0.400

Asia WGS AF: 0.399 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.5
DANN	Benign	0.64
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs1981272; hg19: chr13-106170002;