15-93710025-T-C

Position:

• chr15-93710025-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000554318.2(ENSG00000258631):​n.325-50642T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,240 control chromosomes in the GnomAD database, including 65,457 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 0.93 (65457 hom., cov: 31)
• Consequence: ENSG00000258631 ENST00000554318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532

Genes affected

ENSG00000258631 (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 (NFE) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107983974	XR_001751681.2	n.1033-50642T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258631	ENST00000554318.2	n.325-50642T>C		intron_variant		3
ENSG00000258631	ENST00000653322.1	n.173-50642T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140732 AN: 152122 Hom.: 65412 Cov.: 31

Gnomad AFR AF: 0.826

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.969

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.989

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.967

Gnomad OTH AF: 0.935

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

GnomAD4 genome AF: 0.925 AC: 140829 AN: 152240 Hom.: 65457 Cov.: 31 AF XY: 0.927 AC XY: 68977 AN XY: 74436

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.954

Gnomad4 ASJ AF: 0.969

Gnomad4 EAS AF: 0.915

Gnomad4 SAS AF: 0.925

Gnomad4 FIN AF: 0.989

Gnomad4 NFE AF: 0.967

Gnomad4 OTH AF: 0.930

Alfa AF: 0.960 Hom.: 91140

Bravo AF: 0.918

Asia WGS AF: 0.908 AC: 3160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6497116; hg19: chr15-94253254;