rs2025650

Positions:

• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;