15-96506755-T-C

Position:

• chr15-96506755-T-C

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 0.476 in 151,710 control chromosomes in the GnomAD database, including 17,599 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 0.48 (17599 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.476 AC: 72196 AN: 151598 Hom.: 17592 Cov.: 30

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.500

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.476 AC: 72222 AN: 151710 Hom.: 17599 Cov.: 30 AF XY: 0.476 AC XY: 35287 AN XY: 74102

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.500

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.510

Gnomad4 OTH AF: 0.529

Alfa AF: 0.509 Hom.: 41662

Bravo AF: 0.482

Asia WGS AF: 0.481 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.16
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1370555; hg19: chr15-97049985;