15-94572860-T-G

Position:

• chr15-94572860-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 0.709 in 151,552 control chromosomes in the GnomAD database, including 38,711 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 0.71 (38711 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.94572860T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107347 AN: 151434 Hom.: 38668 Cov.: 30

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.625

Gnomad EAS AF: 0.813

Gnomad SAS AF: 0.774

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.709 AC: 107439 AN: 151552 Hom.: 38711 Cov.: 30 AF XY: 0.711 AC XY: 52645 AN XY: 74056

Gnomad4 AFR AF: 0.776

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.625

Gnomad4 EAS AF: 0.813

Gnomad4 SAS AF: 0.773

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.693

Alfa AF: 0.690 Hom.: 18733

Bravo AF: 0.712

Asia WGS AF: 0.787 AC: 2736 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.65
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1863095; hg19: chr15-95116089;