15-39281334-A-G

Variant names:

• chr15-39281334-A-G
• rs12595668
• ENST00000558209.1:n.451+78455T>C

Variant summary

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

The ENST00000558209.1(ENSG00000259345):​n.451+78455T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,102 control chromosomes in the GnomAD database, including 3,414 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 0.19 (3414 hom., cov: 32)
• Consequence: ENSG00000259345 ENST00000558209.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.549
• 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 = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370777	XR_007064588.1	n.517+139210T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259345	ENST00000558209.1	n.451+78455T>C		intron_variant	Intron 2 of 2	3
ENSG00000259345	ENST00000560484.1	n.67+139575T>C		intron_variant	Intron 1 of 3	4

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28456 AN: 151984 Hom.: 3410 Cov.: 32

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.0951

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.187 AC: 28492 AN: 152102 Hom.: 3414 Cov.: 32 AF XY: 0.183 AC XY: 13595 AN XY: 74358

African (AFR) AF: 0.349 AC: 14453 AN: 41454

American (AMR) AF: 0.108 AC: 1644 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 470 AN: 3468

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5184

South Asian (SAS) AF: 0.0940 AC: 453 AN: 4820

European-Finnish (FIN) AF: 0.158 AC: 1669 AN: 10576

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9229 AN: 68004

Other (OTH) AF: 0.162 AC: 342 AN: 2108

Alfa AF: 0.147 Hom.: 2877

Bravo AF: 0.193

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.84
DANN	Benign	0.71
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs12595668; hg19: chr15-39573535;