rs4924346

Variant names:

• chr15-39347791-G-A
• rs4924346
• ENST00000558209.1:n.451+11998C>T

Your query was ambiguous. Multiple possible variants found:

• chr15-39347791-G-A
• chr15-39347791-G-T

Variant summary

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

The ENST00000558209.1(ENSG00000259345):​n.451+11998C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0909 in 152,058 control chromosomes in the GnomAD database, including 634 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 0.091 (634 hom., cov: 32)
• Consequence: ENSG00000259345 ENST00000558209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 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.451+11998C>T		intron	N/A
	ENSG00000259345	ENST00000559318.1	TSL:4	n.409-48309C>T		intron	N/A
	ENSG00000259345	ENST00000560484.1	TSL:4	n.67+73118C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13820 AN: 151938 Hom.: 635 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0698

Gnomad ASJ AF: 0.0911

Gnomad EAS AF: 0.0419

Gnomad SAS AF: 0.0946

Gnomad FIN AF: 0.0830

Gnomad MID AF: 0.0897

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.0835

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

GnomAD4 genome AF: 0.0909 AC: 13825 AN: 152058 Hom.: 634 Cov.: 32 AF XY: 0.0897 AC XY: 6670 AN XY: 74336

African (AFR) AF: 0.110 AC: 4540 AN: 41452

American (AMR) AF: 0.0695 AC: 1061 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0911 AC: 316 AN: 3470

East Asian (EAS) AF: 0.0418 AC: 217 AN: 5188

South Asian (SAS) AF: 0.0944 AC: 455 AN: 4818

European-Finnish (FIN) AF: 0.0830 AC: 877 AN: 10562

Middle Eastern (MID) AF: 0.0856 AC: 25 AN: 292

European-Non Finnish (NFE) AF: 0.0889 AC: 6042 AN: 67998

Other (OTH) AF: 0.0845 AC: 178 AN: 2106

Alfa AF: 0.0435 Hom.: 35

Bravo AF: 0.0907

Asia WGS AF: 0.0720 AC: 250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.5
DANN	Benign	0.64
PhyloP100		0.083

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: rs4924346;

hg19: chr15-39639992;