13-73117099-G-A

Variant names:

• chr13-73117099-G-A
• rs1333099

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.497 AC: 20590 AN: 41442

American (AMR) AF: 0.551 AC: 8420 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1369 AN: 3470

East Asian (EAS) AF: 0.826 AC: 4266 AN: 5162

South Asian (SAS) AF: 0.625 AC: 3012 AN: 4818

European-Finnish (FIN) AF: 0.524 AC: 5523 AN: 10544

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26643 AN: 67964

Other (OTH) AF: 0.471 AC: 994 AN: 2112

Alfa AF: 0.419 Hom.: 48971

Bravo AF: 0.474

Asia WGS AF: 0.714 AC: 2479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.9
DANN	Benign	0.56
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1333099; hg19: chr13-73691236;