13-64279410-C-T

Variant names:

• chr13-64279410-C-T
• rs1545963

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 0.501 in 151,388 control chromosomes in the GnomAD database, including 20,155 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 0.50 (20155 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 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: 0.501 AC: 75853 AN: 151264 Hom.: 20136 Cov.: 33

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.460

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.501 AC: 75917 AN: 151388 Hom.: 20155 Cov.: 33 AF XY: 0.499 AC XY: 36884 AN XY: 73964

African (AFR) AF: 0.689 AC: 28543 AN: 41432

American (AMR) AF: 0.390 AC: 5922 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1457 AN: 3466

East Asian (EAS) AF: 0.503 AC: 2585 AN: 5136

South Asian (SAS) AF: 0.469 AC: 2246 AN: 4794

European-Finnish (FIN) AF: 0.425 AC: 4448 AN: 10478

Middle Eastern (MID) AF: 0.458 AC: 108 AN: 236

European-Non Finnish (NFE) AF: 0.433 AC: 29283 AN: 67672

Other (OTH) AF: 0.499 AC: 1044 AN: 2092

Alfa AF: 0.319 Hom.: 864

Bravo AF: 0.502

Asia WGS AF: 0.537 AC: 1843 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.11
DANN	Benign	0.47
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1545963; hg19: chr13-64853542;