chr13-42523989-T-A

Variant names:

• chr13-42523989-T-A
• rs2025650

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 0.709 in 152,116 control chromosomes in the GnomAD database, including 38,497 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 0.71 (38497 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.787 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: 0.709 AC: 107808 AN: 151998 Hom.: 38480 Cov.: 33

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.632

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.709 AC: 107865 AN: 152116 Hom.: 38497 Cov.: 33 AF XY: 0.705 AC XY: 52399 AN XY: 74350

African (AFR) AF: 0.665 AC: 27588 AN: 41488

American (AMR) AF: 0.799 AC: 12216 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 2488 AN: 3470

East Asian (EAS) AF: 0.770 AC: 3997 AN: 5188

South Asian (SAS) AF: 0.665 AC: 3200 AN: 4810

European-Finnish (FIN) AF: 0.632 AC: 6668 AN: 10556

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49327 AN: 67996

Other (OTH) AF: 0.719 AC: 1515 AN: 2108

Alfa AF: 0.717 Hom.: 4887

Bravo AF: 0.726

Asia WGS AF: 0.695 AC: 2416 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.43
DANN	Benign	0.53
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2025650; hg19: chr13-43098125;