chr13-36598789-G-A

Variant names:

• chr13-36598789-G-A
• rs673064

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 0.938 in 152,284 control chromosomes in the GnomAD database, including 67,401 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 0.94 (67401 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.938 AC: 142757 AN: 152166 Hom.: 67371 Cov.: 33

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.976

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.994

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.992

Gnomad OTH AF: 0.952

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

GnomAD4 genome AF: 0.938 AC: 142837 AN: 152284 Hom.: 67401 Cov.: 33 AF XY: 0.938 AC XY: 69850 AN XY: 74458

African (AFR) AF: 0.826 AC: 34327 AN: 41534

American (AMR) AF: 0.976 AC: 14933 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3430 AN: 3472

East Asian (EAS) AF: 0.877 AC: 4539 AN: 5174

South Asian (SAS) AF: 0.914 AC: 4405 AN: 4820

European-Finnish (FIN) AF: 0.994 AC: 10562 AN: 10622

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.992 AC: 67479 AN: 68044

Other (OTH) AF: 0.952 AC: 2012 AN: 2114

Alfa AF: 0.965 Hom.: 106160

Bravo AF: 0.932

Asia WGS AF: 0.902 AC: 3136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.13
DANN	Benign	0.61
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs673064; hg19: chr13-37172926;