13-64534408-A-G

Variant names:

• chr13-64534408-A-G
• rs1932762

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 0.948 in 151,832 control chromosomes in the GnomAD database, including 68,390 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 0.95 (68390 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.948 AC: 143758 AN: 151714 Hom.: 68334 Cov.: 30

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.977

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.987

Gnomad SAS AF: 0.970

Gnomad FIN AF: 0.968

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.980

Gnomad OTH AF: 0.965

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

GnomAD4 genome AF: 0.948 AC: 143873 AN: 151832 Hom.: 68390 Cov.: 30 AF XY: 0.948 AC XY: 70368 AN XY: 74204

African (AFR) AF: 0.868 AC: 35949 AN: 41424

American (AMR) AF: 0.977 AC: 14865 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.974 AC: 3377 AN: 3466

East Asian (EAS) AF: 0.987 AC: 5049 AN: 5116

South Asian (SAS) AF: 0.970 AC: 4678 AN: 4822

European-Finnish (FIN) AF: 0.968 AC: 10279 AN: 10618

Middle Eastern (MID) AF: 0.986 AC: 290 AN: 294

European-Non Finnish (NFE) AF: 0.980 AC: 66521 AN: 67866

Other (OTH) AF: 0.965 AC: 2031 AN: 2104

Alfa AF: 0.962 Hom.: 118360

Bravo AF: 0.945

Asia WGS AF: 0.978 AC: 3398 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.85
DANN	Benign	0.36
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs1932762; hg19: chr13-65108540;