rs17525472

Variant names:

• chr15-51677471-T-C
• rs17525472
• ENST00000746672.1:n.346+3613A>G

Variant summary

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

The ENST00000746672.1(ENSG00000297267):​n.346+3613A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.099 in 152,268 control chromosomes in the GnomAD database, including 1,051 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 0.099 (1051 hom., cov: 32)
• Consequence: ENSG00000297267 ENST00000746672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469
• Publications: 17 publications found

Genes affected

ENSG00000297267 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746672.1. 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
	ENSG00000297267	ENST00000746672.1		n.346+3613A>G		intron	N/A
	ENSG00000297287	ENST00000746809.1		n.-191T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.0990 AC: 15062 AN: 152150 Hom.: 1046 Cov.: 32

Gnomad AFR AF: 0.0404

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.00288

Gnomad SAS AF: 0.0854

Gnomad FIN AF: 0.0627

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.0990 AC: 15075 AN: 152268 Hom.: 1051 Cov.: 32 AF XY: 0.0973 AC XY: 7242 AN XY: 74450

African (AFR) AF: 0.0403 AC: 1674 AN: 41572

American (AMR) AF: 0.215 AC: 3284 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3468

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5190

South Asian (SAS) AF: 0.0852 AC: 411 AN: 4822

European-Finnish (FIN) AF: 0.0627 AC: 665 AN: 10608

Middle Eastern (MID) AF: 0.113 AC: 33 AN: 292

European-Non Finnish (NFE) AF: 0.122 AC: 8273 AN: 68008

Other (OTH) AF: 0.116 AC: 246 AN: 2112

Alfa AF: 0.114 Hom.: 2431

Bravo AF: 0.110

Asia WGS AF: 0.0510 AC: 176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.3
DANN	Benign	0.88
PhyloP100		0.47

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: rs17525472;

hg19: chr15-51969668;