rs2025650

Variant names:

• chr13-42523989-T-A
• rs2025650

Your query was ambiguous. Multiple possible variants found:

• chr13-42523989-T-A
• chr13-42523989-T-C
• chr13-42523989-T-G

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 0.709 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.709 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

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.799

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.770

Gnomad4 SAS AF: 0.665

Gnomad4 FIN AF: 0.632

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.719

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2025650; hg19: chr13-43098125;