chr13-73117099-G-A

Position:

• chr13-73117099-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 0.468 in 151,994 control chromosomes in the GnomAD database, including 17,458 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 0.47 (17458 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.254

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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: 0.468 AC: 71133 AN: 151876 Hom.: 17437 Cov.: 32

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.468 AC: 71196 AN: 151994 Hom.: 17458 Cov.: 32 AF XY: 0.482 AC XY: 35769 AN XY: 74280

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.826

Gnomad4 SAS AF: 0.625

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.471

Alfa AF: 0.417 Hom.: 20275

Bravo AF: 0.474

Asia WGS AF: 0.714 AC: 2479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1333099; hg19: chr13-73691236;