ENST00000558209.1:n.98+9322A>G

Variant names:

• chr15-39417776-T-C
• rs4344715
• ENST00000558209.1:n.98+9322A>G

Variant summary

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

The ENST00000558209.1(ENSG00000259345):​n.98+9322A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.808 in 152,246 control chromosomes in the GnomAD database, including 50,151 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 0.81 (50151 hom., cov: 34)
• Consequence: ENSG00000259345 ENST00000558209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67
• Publications: 3 publications found

Genes affected

ENSG00000259345 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000558209.1. 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
	ENSG00000259345	ENST00000558209.1	TSL:3	n.98+9322A>G		intron	N/A
	ENSG00000259345	ENST00000559318.1	TSL:4	n.408+2768A>G		intron	N/A
	ENSG00000259345	ENST00000560484.1	TSL:4	n.67+3133A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.808 AC: 122963 AN: 152128 Hom.: 50093 Cov.: 34

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.781

Gnomad OTH AF: 0.806

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

GnomAD4 genome AF: 0.808 AC: 123081 AN: 152246 Hom.: 50151 Cov.: 34 AF XY: 0.804 AC XY: 59838 AN XY: 74438

African (AFR) AF: 0.896 AC: 37240 AN: 41550

American (AMR) AF: 0.786 AC: 12019 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2947 AN: 3472

East Asian (EAS) AF: 0.727 AC: 3770 AN: 5186

South Asian (SAS) AF: 0.790 AC: 3807 AN: 4822

European-Finnish (FIN) AF: 0.702 AC: 7437 AN: 10590

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.781 AC: 53147 AN: 68020

Other (OTH) AF: 0.808 AC: 1708 AN: 2114

Alfa AF: 0.788 Hom.: 23962

Bravo AF: 0.818

Asia WGS AF: 0.781 AC: 2714 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.035
DANN	Benign	0.62
PhyloP100		-2.7

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: rs4344715;

hg19: chr15-39709977;