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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370777	XR_007064588.1	n.517+72753C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259345	ENST00000558209.1	n.451+11998C>T		intron_variant	Intron 2 of 2	3
ENSG00000259345	ENST00000559318.1	n.409-48309C>T		intron_variant	Intron 1 of 1	4
ENSG00000259345	ENST00000560484.1	n.67+73118C>T		intron_variant	Intron 1 of 3	4

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 v4.3

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

Other links and lift over

dbSNP: rs4924346; hg19: chr15-39639992;