13-28299518-C-A

Position:

• chr13-28299518-C-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.157

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.272

Alfa AF: 0.271 Hom.: 1084

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17086497; hg19: chr13-28873655;