ENST00000811935.1:n.117-2790G>A

Variant names:

• chr15-88575873-G-A
• rs17776563
• ENST00000811935.1:n.117-2790G>A

Variant summary

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

The ENST00000811935.1(ENSG00000305611):​n.117-2790G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,126 control chromosomes in the GnomAD database, including 4,895 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 0.23 (4895 hom., cov: 32)
• Consequence: ENSG00000305611 ENST00000811935.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 18 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 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.117-2790G>A		intron_variant	Intron 1 of 2
ENSG00000305611	ENST00000811936.1	n.109-2790G>A		intron_variant	Intron 1 of 2
ENSG00000305611	ENST00000811937.1	n.81-2786G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34493 AN: 152008 Hom.: 4900 Cov.: 32

Gnomad AFR AF: 0.0588

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.227 AC: 34483 AN: 152126 Hom.: 4895 Cov.: 32 AF XY: 0.225 AC XY: 16700 AN XY: 74344

African (AFR) AF: 0.0586 AC: 2436 AN: 41548

American (AMR) AF: 0.226 AC: 3452 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3468

East Asian (EAS) AF: 0.197 AC: 1016 AN: 5152

South Asian (SAS) AF: 0.144 AC: 697 AN: 4824

European-Finnish (FIN) AF: 0.320 AC: 3374 AN: 10558

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21529 AN: 67974

Other (OTH) AF: 0.267 AC: 562 AN: 2108

Alfa AF: 0.265 Hom.: 8849

Bravo AF: 0.214

Asia WGS AF: 0.160 AC: 554 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	0.30
DANN	Benign	0.42
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17776563; hg19: chr15-89119104;