13-42669655-T-A

Position:

• chr13-42669655-T-A

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 0.815 in 152,180 control chromosomes in the GnomAD database, including 51,535 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 0.81 (51535 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.454

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 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: 0.815 AC: 123906 AN: 152062 Hom.: 51521 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.902

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.832

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

GnomAD4 genome AF: 0.815 AC: 123956 AN: 152180 Hom.: 51535 Cov.: 32 AF XY: 0.815 AC XY: 60641 AN XY: 74404

Gnomad4 AFR AF: 0.643

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.902

Gnomad4 FIN AF: 0.946

Gnomad4 NFE AF: 0.904

Gnomad4 OTH AF: 0.836

Alfa AF: 0.854 Hom.: 6979

Bravo AF: 0.789

Asia WGS AF: 0.818 AC: 2846 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.0
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9533208; hg19: chr13-43243791;