chr13-97136192-G-A

Position:

• chr13-97136192-G-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 0.099 in 152,120 control chromosomes in the GnomAD database, including 870 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 0.099 (870 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 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: 0.0990 AC: 15050 AN: 152002 Hom.: 872 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0688

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.0990 AC: 15061 AN: 152120 Hom.: 870 Cov.: 32 AF XY: 0.103 AC XY: 7630 AN XY: 74350

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0948

Gnomad4 NFE AF: 0.0688

Gnomad4 OTH AF: 0.102

Alfa AF: 0.0721 Hom.: 521

Bravo AF: 0.100

Asia WGS AF: 0.188 AC: 653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2282424; hg19: chr13-97788446;