rs13174919

Positions:

• chr5-1299747-G-C

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 0.278 in 151,794 control chromosomes in the GnomAD database, including 6,116 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 (6116 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 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: 0.278 AC: 42160 AN: 151676 Hom.: 6111 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.278 AC: 42192 AN: 151794 Hom.: 6116 Cov.: 32 AF XY: 0.282 AC XY: 20952 AN XY: 74186

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.254

Alfa AF: 0.286 Hom.: 804

Bravo AF: 0.281

Asia WGS AF: 0.387 AC: 1345 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.88
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13174919; hg19: chr5-1299862; COSMIC: COSV57244866;