chr13-64376290-T-C

Variant names:

• chr13-64376290-T-C
• rs1340319

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 0.43 in 151,968 control chromosomes in the GnomAD database, including 14,442 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 0.43 (14442 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.512 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: 0.429 AC: 65215 AN: 151852 Hom.: 14416 Cov.: 32

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.430 AC: 65294 AN: 151968 Hom.: 14442 Cov.: 32 AF XY: 0.425 AC XY: 31552 AN XY: 74276

African (AFR) AF: 0.414 AC: 17147 AN: 41460

American (AMR) AF: 0.521 AC: 7954 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1425 AN: 3466

East Asian (EAS) AF: 0.236 AC: 1217 AN: 5158

South Asian (SAS) AF: 0.391 AC: 1881 AN: 4814

European-Finnish (FIN) AF: 0.307 AC: 3240 AN: 10564

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.455 AC: 30919 AN: 67938

Other (OTH) AF: 0.435 AC: 916 AN: 2108

Alfa AF: 0.446 Hom.: 5170

Bravo AF: 0.445

Asia WGS AF: 0.372 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.28
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1340319; hg19: chr13-64950422;