13-101417809-T-A

Variant names:

• chr13-101417809-T-A
• rs2152324

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.866

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.879

Gnomad4 FIN AF: 0.876

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.856

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2152324; hg19: chr13-102070160;