15-87668715-T-C

Variant names:

• chr15-87668715-T-C
• rs10468137
• ENST00000560439.1:n.80+35058A>G

Variant summary

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

The ENST00000560439.1(ENSG00000259560):​n.80+35058A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 152,146 control chromosomes in the GnomAD database, including 37,155 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 0.70 (37155 hom., cov: 33)
• Consequence: ENSG00000259560 ENST00000560439.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.764
• Publications: 4 publications found

Genes affected

ENSG00000259560 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724465	NR_187944.1	n.83+35058A>G		intron_variant	Intron 1 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259560	ENST00000560439.1	n.80+35058A>G		intron_variant	Intron 1 of 5	3
ENSG00000259560	ENST00000656130.2	n.85+35058A>G		intron_variant	Intron 1 of 4
ENSG00000259560	ENST00000665121.1	n.53+35058A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105742 AN: 152028 Hom.: 37133 Cov.: 33

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.697

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.695 AC: 105805 AN: 152146 Hom.: 37155 Cov.: 33 AF XY: 0.692 AC XY: 51479 AN XY: 74372

African (AFR) AF: 0.775 AC: 32176 AN: 41520

American (AMR) AF: 0.577 AC: 8822 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2066 AN: 3466

East Asian (EAS) AF: 0.697 AC: 3600 AN: 5162

South Asian (SAS) AF: 0.616 AC: 2972 AN: 4824

European-Finnish (FIN) AF: 0.729 AC: 7715 AN: 10578

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46371 AN: 67992

Other (OTH) AF: 0.667 AC: 1407 AN: 2110

Alfa AF: 0.668 Hom.: 38646

Bravo AF: 0.687

Asia WGS AF: 0.648 AC: 2253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.0
DANN	Benign	0.20
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs10468137; hg19: chr15-88211946;