17-15017748-C-T

Variant names:

• chr17-15017748-C-T
• rs917541
• ENST00000446671.2:n.108+2890C>T

Variant summary

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

The ENST00000446671.2(ENSG00000232058):​n.108+2890C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,982 control chromosomes in the GnomAD database, including 17,723 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 (17723 hom., cov: 32)
• Consequence: ENSG00000232058 ENST00000446671.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 6 publications found

Genes affected

ENSG00000232058 (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 (NFE) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446671.2. 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
	LOC101928475	NR_135638.1		n.54+2890C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000232058	ENST00000446671.2	TSL:1	n.108+2890C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73177 AN: 151864 Hom.: 17722 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.482 AC: 73226 AN: 151982 Hom.: 17723 Cov.: 32 AF XY: 0.483 AC XY: 35896 AN XY: 74264

African (AFR) AF: 0.450 AC: 18668 AN: 41454

American (AMR) AF: 0.463 AC: 7067 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1572 AN: 3470

East Asian (EAS) AF: 0.461 AC: 2371 AN: 5144

South Asian (SAS) AF: 0.459 AC: 2207 AN: 4812

European-Finnish (FIN) AF: 0.536 AC: 5663 AN: 10564

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33999 AN: 67954

Other (OTH) AF: 0.495 AC: 1044 AN: 2108

Alfa AF: 0.492 Hom.: 57583

Bravo AF: 0.479

Asia WGS AF: 0.437 AC: 1524 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	0.83
DANN	Benign	0.77
PhyloP100		0.013

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs917541;

hg19: chr17-14921065;