15-93710025-T-C

Variant names:

• chr15-93710025-T-C
• rs6497116
• ENST00000554318.2:n.325-50642T>C

Variant summary

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

The ENST00000554318.2(ENSG00000257060):​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: ENSG00000257060 ENST00000554318.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.532
• Publications: 2 publications found

Genes affected

ENSG00000257060 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554318.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257060	ENST00000554318.2	TSL:3	n.325-50642T>C		intron	N/A
	ENSG00000257060	ENST00000653322.2		n.1089-50642T>C		intron	N/A

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

African (AFR) AF: 0.826 AC: 34267 AN: 41504

American (AMR) AF: 0.954 AC: 14583 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.969 AC: 3366 AN: 3472

East Asian (EAS) AF: 0.915 AC: 4742 AN: 5182

South Asian (SAS) AF: 0.925 AC: 4456 AN: 4816

European-Finnish (FIN) AF: 0.989 AC: 10506 AN: 10620

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.967 AC: 65774 AN: 68034

Other (OTH) AF: 0.930 AC: 1965 AN: 2114

Alfa AF: 0.956 Hom.: 114667

Bravo AF: 0.918

Asia WGS AF: 0.908 AC: 3160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.8
DANN	Benign	0.78
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs6497116; hg19: chr15-94253254;