15-79721080-T-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 0.666 in 152,000 control chromosomes in the GnomAD database, including 34,475 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 0.67 (34475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 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: 0.666 AC: 101161 AN: 151882 Hom.: 34420 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.635

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.666 AC: 101272 AN: 152000 Hom.: 34475 Cov.: 32 AF XY: 0.658 AC XY: 48900 AN XY: 74270

Gnomad4 AFR AF: 0.786

Gnomad4 AMR AF: 0.706

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.635

Gnomad4 OTH AF: 0.670

Alfa AF: 0.564 Hom.: 2050

Bravo AF: 0.687

Asia WGS AF: 0.513 AC: 1785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.075
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2692194; hg19: chr15-80013422; COSMIC: COSV68084056;