rs1829758

chr15-80028609-C-Achr15-80028609-C-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;