13-34739364-C-T

Variant names:

• chr13-34739364-C-T
• rs9564594

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 0.22 in 152,034 control chromosomes in the GnomAD database, including 4,522 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 0.22 (4522 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.965
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.301 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: 0.220 AC: 33410 AN: 151916 Hom.: 4522 Cov.: 32

Gnomad AFR AF: 0.0619

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.220 AC: 33399 AN: 152034 Hom.: 4522 Cov.: 32 AF XY: 0.226 AC XY: 16760 AN XY: 74282

African (AFR) AF: 0.0618 AC: 2564 AN: 41498

American (AMR) AF: 0.303 AC: 4622 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 948 AN: 3472

East Asian (EAS) AF: 0.293 AC: 1507 AN: 5142

South Asian (SAS) AF: 0.314 AC: 1510 AN: 4812

European-Finnish (FIN) AF: 0.309 AC: 3262 AN: 10542

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18059 AN: 67992

Other (OTH) AF: 0.215 AC: 454 AN: 2112

Alfa AF: 0.254 Hom.: 6574

Bravo AF: 0.211

Asia WGS AF: 0.272 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.72
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs9564594; hg19: chr13-35313501;