chr13-101417809-T-A

Variant names:

• chr13-101417809-T-A
• rs2152324

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 0.872 in 152,236 control chromosomes in the GnomAD database, including 58,023 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 0.87 (58023 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132588 AN: 152118 Hom.: 57979 Cov.: 33

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.796

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.878

Gnomad FIN AF: 0.876

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.861

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

GnomAD4 genome AF: 0.872 AC: 132689 AN: 152236 Hom.: 58023 Cov.: 33 AF XY: 0.873 AC XY: 64960 AN XY: 74434

African (AFR) AF: 0.926 AC: 38477 AN: 41556

American (AMR) AF: 0.795 AC: 12161 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3006 AN: 3472

East Asian (EAS) AF: 0.746 AC: 3853 AN: 5168

South Asian (SAS) AF: 0.879 AC: 4246 AN: 4832

European-Finnish (FIN) AF: 0.876 AC: 9273 AN: 10590

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.863 AC: 58727 AN: 68012

Other (OTH) AF: 0.856 AC: 1807 AN: 2112

Alfa AF: 0.870 Hom.: 7163

Bravo AF: 0.863

Asia WGS AF: 0.821 AC: 2850 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.77
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs2152324; hg19: chr13-102070160;