15-45736425-A-T

Variant names:

• chr15-45736425-A-T
• rs16947598
• ENST00000559600.1:n.95+31136A>T

Variant summary

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

The ENST00000559600.1(ENSG00000259200):​n.95+31136A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0939 in 152,188 control chromosomes in the GnomAD database, including 1,063 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 0.094 (1063 hom., cov: 32)
• Consequence: ENSG00000259200 ENST00000559600.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600
• Publications: 1 publications found

Genes affected

ENSG00000259200 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000559600.1. 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
	LOC105370802	NR_135680.1		n.95+31136A>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000259200	ENST00000559600.1	TSL:3	n.95+31136A>T		intron	N/A
	ENSG00000259200	ENST00000560705.1	TSL:3	n.317+29655A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0940 AC: 14287 AN: 152070 Hom.: 1065 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0457

Gnomad ASJ AF: 0.0649

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0525

Gnomad OTH AF: 0.0817

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

GnomAD4 genome AF: 0.0939 AC: 14296 AN: 152188 Hom.: 1063 Cov.: 32 AF XY: 0.0941 AC XY: 7006 AN XY: 74422

African (AFR) AF: 0.199 AC: 8261 AN: 41500

American (AMR) AF: 0.0457 AC: 698 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0649 AC: 225 AN: 3468

East Asian (EAS) AF: 0.0178 AC: 92 AN: 5174

South Asian (SAS) AF: 0.0205 AC: 99 AN: 4822

European-Finnish (FIN) AF: 0.107 AC: 1138 AN: 10606

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0524 AC: 3565 AN: 68010

Other (OTH) AF: 0.0808 AC: 171 AN: 2116

Alfa AF: 0.0176 Hom.: 11

Bravo AF: 0.0944

Asia WGS AF: 0.0340 AC: 120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.78
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs16947598; hg19: chr15-46028623;