rs17117533

Variant names:

• chr15-23781462-G-C
• rs17117533
• ENST00000658937.1:n.459+23889G>C

Your query was ambiguous. Multiple possible variants found:

• chr15-23781462-G-C
• chr15-23781462-G-T

Variant summary

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

The ENST00000658937.1(ENSG00000286973):​n.459+23889G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,112 control chromosomes in the GnomAD database, including 3,894 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 0.22 (3894 hom., cov: 32)
• Consequence: ENSG00000286973 ENST00000658937.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245

Genes affected

ENSG00000286973 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286973	ENST00000658937.1	n.459+23889G>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33266 AN: 151994 Hom.: 3894 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.0252

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.219 AC: 33265 AN: 152112 Hom.: 3894 Cov.: 32 AF XY: 0.219 AC XY: 16292 AN XY: 74354

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.158

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.0251

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.188

Alfa AF: 0.0747 Hom.: 99

Bravo AF: 0.212

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.0
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: rs17117533; hg19: chr15-24026609;