15-80028609-C-A

Variant names:

• chr15-80028609-C-A
• rs1829758

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 0.826 in 152,092 control chromosomes in the GnomAD database, including 52,153 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 0.83 (52153 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 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: 0.826 AC: 125476 AN: 151974 Hom.: 52096 Cov.: 30

Gnomad AFR AF: 0.902

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.730

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.826 AC: 125590 AN: 152092 Hom.: 52153 Cov.: 30 AF XY: 0.821 AC XY: 61003 AN XY: 74322

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.843

Gnomad4 ASJ AF: 0.730

Gnomad4 EAS AF: 0.679

Gnomad4 SAS AF: 0.779

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.823

Alfa AF: 0.820 Hom.: 11603

Bravo AF: 0.837

Asia WGS AF: 0.715 AC: 2488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.19
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1829758; hg19: chr15-80320951;