chr13-42543065-C-T

Position:

• chr13-42543065-C-T

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 0.179 in 152,078 control chromosomes in the GnomAD database, including 2,641 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 0.18 (2641 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.474

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.291 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: 0.179 AC: 27154 AN: 151960 Hom.: 2630 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.179 AC: 27182 AN: 152078 Hom.: 2641 Cov.: 32 AF XY: 0.178 AC XY: 13210 AN XY: 74350

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.129

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.181

Alfa AF: 0.142 Hom.: 402

Bravo AF: 0.195

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17596685; hg19: chr13-43117201;