13-73334709-C-G

Position:

• chr13-73334709-C-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 0.523 in 152,082 control chromosomes in the GnomAD database, including 24,413 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 0.52 (24413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.674 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: 0.524 AC: 79591 AN: 151964 Hom.: 24422 Cov.: 32

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.523 AC: 79580 AN: 152082 Hom.: 24413 Cov.: 32 AF XY: 0.525 AC XY: 39042 AN XY: 74354

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.568

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.679

Gnomad4 OTH AF: 0.527

Alfa AF: 0.645 Hom.: 17850

Bravo AF: 0.504

Asia WGS AF: 0.584 AC: 2033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	0.21
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9573163; hg19: chr13-73908846;