chr5-1299747-G-C

Variant names:

• chr5-1299747-G-C
• rs13174919

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;