chr15-39336202-G-A

Variant names:

• chr15-39336202-G-A
• rs11070192
• ENST00000558209.1:n.451+23587C>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+23587C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.799 in 152,186 control chromosomes in the GnomAD database, including 49,029 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 0.80 (49029 hom., cov: 32)
• Consequence: ENSG00000259345 ENST00000558209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370777	XR_007064588.1	n.517+84342C>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+23587C>T		intron_variant	Intron 2 of 2	3
ENSG00000259345	ENST00000559318.1	n.409-36720C>T		intron_variant	Intron 1 of 1	4
ENSG00000259345	ENST00000560484.1	n.67+84707C>T		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.799 AC: 121563 AN: 152068 Hom.: 48997 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.865

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.799 AC: 121643 AN: 152186 Hom.: 49029 Cov.: 32 AF XY: 0.794 AC XY: 59118 AN XY: 74412

African (AFR) AF: 0.725 AC: 30066 AN: 41480

American (AMR) AF: 0.735 AC: 11243 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.865 AC: 3001 AN: 3470

East Asian (EAS) AF: 0.665 AC: 3441 AN: 5176

South Asian (SAS) AF: 0.808 AC: 3898 AN: 4824

European-Finnish (FIN) AF: 0.811 AC: 8590 AN: 10592

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58535 AN: 68024

Other (OTH) AF: 0.816 AC: 1725 AN: 2114

Alfa AF: 0.816 Hom.: 13896

Bravo AF: 0.787

Asia WGS AF: 0.745 AC: 2592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.2
DANN	Benign	0.45
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs11070192; hg19: chr15-39628403;