15-96506755-T-C

Variant names:

• chr15-96506755-T-C
• rs1370555
• ENST00000751179.1:n.238-13647A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000751179.1(ENSG00000297815):​n.238-13647A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000297815 ENST00000751179.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 2 publications found

Genes affected

ENSG00000297815 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751179.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297815	ENST00000751179.1		n.238-13647A>G		intron	N/A

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

African (AFR) AF: 0.385 AC: 15910 AN: 41344

American (AMR) AF: 0.589 AC: 8972 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1729 AN: 3460

East Asian (EAS) AF: 0.452 AC: 2308 AN: 5108

South Asian (SAS) AF: 0.585 AC: 2813 AN: 4806

European-Finnish (FIN) AF: 0.384 AC: 4048 AN: 10530

Middle Eastern (MID) AF: 0.618 AC: 178 AN: 288

European-Non Finnish (NFE) AF: 0.510 AC: 34642 AN: 67920

Other (OTH) AF: 0.529 AC: 1115 AN: 2108

Alfa AF: 0.500 Hom.: 85172

Bravo AF: 0.482

Asia WGS AF: 0.481 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.16
DANN	Benign	0.47
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1370555; hg19: chr15-97049985;