15-88567604-C-T

Variant names:

• chr15-88567604-C-T
• rs11073790
• ENST00000811935.1:n.117-11059C>T

Variant summary

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

The ENST00000811935.1(ENSG00000305611):​n.117-11059C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,896 control chromosomes in the GnomAD database, including 7,249 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 0.30 (7249 hom., cov: 31)
• Consequence: ENSG00000305611 ENST00000811935.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 10 publications found

Genes affected

ENSG00000305611 (HGNC:):

LINC01586 (HGNC:51434): (long intergenic non-protein coding RNA 1586)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305611	ENST00000811935.1	n.117-11059C>T		intron_variant	Intron 1 of 2
ENSG00000305611	ENST00000811936.1	n.109-11059C>T		intron_variant	Intron 1 of 2
ENSG00000305611	ENST00000811937.1	n.81-11055C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46066 AN: 151778 Hom.: 7250 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.303 AC: 46075 AN: 151896 Hom.: 7249 Cov.: 31 AF XY: 0.299 AC XY: 22165 AN XY: 74202

African (AFR) AF: 0.236 AC: 9776 AN: 41414

American (AMR) AF: 0.258 AC: 3943 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1108 AN: 3470

East Asian (EAS) AF: 0.217 AC: 1119 AN: 5146

South Asian (SAS) AF: 0.201 AC: 968 AN: 4816

European-Finnish (FIN) AF: 0.358 AC: 3772 AN: 10544

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24107 AN: 67922

Other (OTH) AF: 0.330 AC: 696 AN: 2110

Alfa AF: 0.340 Hom.: 14857

Bravo AF: 0.295

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.76
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs11073790; hg19: chr15-89110835;