chr13-82733077-A-G

Position:

• chr13-82733077-A-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 0.13 in 151,796 control chromosomes in the GnomAD database, including 1,368 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 0.13 (1368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.942

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.147 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: 0.130 AC: 19716 AN: 151678 Hom.: 1364 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0531

Gnomad EAS AF: 0.0141

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.130 AC: 19746 AN: 151796 Hom.: 1368 Cov.: 32 AF XY: 0.130 AC XY: 9645 AN XY: 74212

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0531

Gnomad4 EAS AF: 0.0141

Gnomad4 SAS AF: 0.0945

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.126

Alfa AF: 0.135 Hom.: 1618

Bravo AF: 0.124

Asia WGS AF: 0.0590 AC: 206 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17259922; hg19: chr13-83307212;