rs2270059

Variant names:

• chr15-92172716-C-A
• rs2270059
• ENST00000561674.1:n.186-15475G>T

Your query was ambiguous. Multiple possible variants found:

• chr15-92172716-C-A
• chr15-92172716-C-T

Variant summary

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

The ENST00000561674.1(ENSG00000260661):​n.186-15475G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,078 control chromosomes in the GnomAD database, including 13,071 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 0.41 (13071 hom., cov: 32)
• Consequence: ENSG00000260661 ENST00000561674.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

Genes affected

ENSG00000260661 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 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
ENSG00000260661	ENST00000561674.1	n.186-15475G>T		intron_variant	Intron 2 of 3	1

Frequencies

GnomAD3 genomes AF: 0.405 AC: 61618 AN: 151960 Hom.: 13047 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.414

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.406 AC: 61690 AN: 152078 Hom.: 13071 Cov.: 32 AF XY: 0.405 AC XY: 30140 AN XY: 74356

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.329

Gnomad4 OTH AF: 0.416

Alfa AF: 0.344 Hom.: 12038

Bravo AF: 0.427

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2270059; hg19: chr15-92715946;