chr13-28299518-C-A

Variant names:

• chr13-28299518-C-A
• rs17086497

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 0.279 in 151,984 control chromosomes in the GnomAD database, including 6,654 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 0.28 (6654 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 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: 0.279 AC: 42353 AN: 151866 Hom.: 6642 Cov.: 32

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.157

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.279 AC: 42400 AN: 151984 Hom.: 6654 Cov.: 32 AF XY: 0.277 AC XY: 20547 AN XY: 74274

African (AFR) AF: 0.427 AC: 17700 AN: 41416

American (AMR) AF: 0.200 AC: 3047 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 540 AN: 3470

East Asian (EAS) AF: 0.340 AC: 1759 AN: 5170

South Asian (SAS) AF: 0.157 AC: 756 AN: 4826

European-Finnish (FIN) AF: 0.241 AC: 2539 AN: 10550

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15302 AN: 67972

Other (OTH) AF: 0.272 AC: 573 AN: 2110

Alfa AF: 0.276 Hom.: 1163

Bravo AF: 0.283

Asia WGS AF: 0.254 AC: 885 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	4.6
DANN	Benign	0.84
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs17086497; hg19: chr13-28873655;