17-15396028-A-G

Variant names:

• chr17-15396028-A-G
• rs2024158
• ENST00000580422.1:n.315-13907T>C

Variant summary

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

The ENST00000580422.1(ENSG00000266667):​n.315-13907T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.935 in 152,050 control chromosomes in the GnomAD database, including 66,737 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 0.94 (66737 hom., cov: 30)
• Consequence: ENSG00000266667 ENST00000580422.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 1 publications found

Genes affected

ENSG00000266667 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000580422.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000266667	ENST00000580422.1	TSL:5	n.315-13907T>C		intron	N/A
	ENSG00000266667	ENST00000762561.1		n.325-13395T>C		intron	N/A
	ENSG00000266667	ENST00000762562.1		n.292-13504T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.936 AC: 142138 AN: 151932 Hom.: 66696 Cov.: 30

Gnomad AFR AF: 0.861

Gnomad AMI AF: 0.963

Gnomad AMR AF: 0.954

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.975

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.935 AC: 142235 AN: 152050 Hom.: 66737 Cov.: 30 AF XY: 0.935 AC XY: 69497 AN XY: 74316

African (AFR) AF: 0.860 AC: 35633 AN: 41412

American (AMR) AF: 0.954 AC: 14581 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.933 AC: 3239 AN: 3472

East Asian (EAS) AF: 0.906 AC: 4653 AN: 5134

South Asian (SAS) AF: 0.900 AC: 4334 AN: 4814

European-Finnish (FIN) AF: 0.973 AC: 10297 AN: 10580

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.975 AC: 66360 AN: 68038

Other (OTH) AF: 0.942 AC: 1988 AN: 2110

Alfa AF: 0.959 Hom.: 78141

Bravo AF: 0.930

Asia WGS AF: 0.897 AC: 3121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.45
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs2024158; hg19: chr17-15299345;