17-15396028-A-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000266667 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000266667	ENST00000580422.1	n.315-13907T>C		intron_variant	Intron 2 of 3	5

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

Gnomad4 AFR AF: 0.860

Gnomad4 AMR AF: 0.954

Gnomad4 ASJ AF: 0.933

Gnomad4 EAS AF: 0.906

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.973

Gnomad4 NFE AF: 0.975

Gnomad4 OTH AF: 0.942

Alfa AF: 0.964 Hom.: 59029

Bravo AF: 0.930

Asia WGS AF: 0.897 AC: 3121 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2024158; hg19: chr17-15299345;