rs917541

chr17-15017748-C-T

Variant summary

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

The ENST00000446671.1(ENSG00000232058):n.54+2890C>T variant causes a intron, non coding transcript 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: ENST00000446671.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130

Genes affected

(HGNC:):

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000446671.1	n.54+2890C>T		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.463

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.459

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.495

Alfa AF: 0.496 Hom.: 37994

Bravo AF: 0.479

Asia WGS AF: 0.437 AC: 1524 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	0.83
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs917541; hg19: chr17-14921065;