13-23004409-C-T

Variant names:

• chr13-23004409-C-T
• rs9510516

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 0.502 in 151,942 control chromosomes in the GnomAD database, including 20,027 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 (20027 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.6 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: 0.502 AC: 76267 AN: 151822 Hom.: 20021 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.502 AC: 76301 AN: 151942 Hom.: 20027 Cov.: 32 AF XY: 0.496 AC XY: 36841 AN XY: 74274

African (AFR) AF: 0.380 AC: 15739 AN: 41420

American (AMR) AF: 0.373 AC: 5689 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2066 AN: 3470

East Asian (EAS) AF: 0.427 AC: 2204 AN: 5164

South Asian (SAS) AF: 0.456 AC: 2199 AN: 4820

European-Finnish (FIN) AF: 0.527 AC: 5551 AN: 10526

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41078 AN: 67964

Other (OTH) AF: 0.528 AC: 1118 AN: 2116

Alfa AF: 0.520 Hom.: 5384

Bravo AF: 0.484

Asia WGS AF: 0.414 AC: 1437 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.14
DANN	Benign	0.52
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs9510516; hg19: chr13-23578548;