15-96957080-G-T

Position:

• chr15-96957080-G-T

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 0.492 in 151,998 control chromosomes in the GnomAD database, including 18,638 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 0.49 (18638 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.96957080G>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74714 AN: 151880 Hom.: 18631 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.492 AC: 74755 AN: 151998 Hom.: 18638 Cov.: 32 AF XY: 0.487 AC XY: 36180 AN XY: 74288

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.484

Gnomad4 OTH AF: 0.491

Alfa AF: 0.480 Hom.: 38816

Bravo AF: 0.503

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.25
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9672547; hg19: chr15-97500310;