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. The variant received -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
• Publications: 7 publications found

Genes affected

ENSG00000260661 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561674.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260661	ENST00000561674.1	TSL:1	n.186-15475G>T		intron	N/A
	ENSG00000260661	ENST00000769885.1		n.273-9228G>T		intron	N/A

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

African (AFR) AF: 0.524 AC: 21707 AN: 41462

American (AMR) AF: 0.478 AC: 7312 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1489 AN: 3472

East Asian (EAS) AF: 0.414 AC: 2142 AN: 5172

South Asian (SAS) AF: 0.356 AC: 1714 AN: 4820

European-Finnish (FIN) AF: 0.351 AC: 3712 AN: 10566

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22396 AN: 67988

Other (OTH) AF: 0.416 AC: 877 AN: 2108

Alfa AF: 0.355 Hom.: 16494

Bravo AF: 0.427

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.61
PhyloP100		0.0060

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: rs2270059;

hg19: chr15-92715946;