13-64534408-A-G

Variant names:

• chr13-64534408-A-G
• rs1932762

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 0.948 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.868

Gnomad4 AMR AF: 0.977

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.987

Gnomad4 SAS AF: 0.970

Gnomad4 FIN AF: 0.968

Gnomad4 NFE AF: 0.980

Gnomad4 OTH AF: 0.965

Alfa AF: 0.974 Hom.: 69643

Bravo AF: 0.945

Asia WGS AF: 0.978 AC: 3398 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1932762; hg19: chr13-65108540;