chr13-64534408-A-G

Position:

• chr13-64534408-A-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 0.948 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;