ENST00000757433.1:n.1108G>A

Variant names:

• chr2-188285126-C-T
• rs9808557
• ENST00000757433.1:n.1108G>A

Variant summary

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

The ENST00000757433.1(LINC01090):​n.1108G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,062 control chromosomes in the GnomAD database, including 5,522 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 0.24 (5522 hom., cov: 33)
• Consequence: LINC01090 ENST00000757433.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75
• Publications: 2 publications found

Genes affected

LINC01090 (HGNC:49201): (long intergenic non-protein coding RNA 1090)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01090	NR_126396.1	n.225+2341G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01090	ENST00000757433.1	n.1108G>A		non_coding_transcript_exon_variant	Exon 2 of 2
LINC01090	ENST00000757434.1	n.618G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LINC01090	ENST00000415357.1	n.168+2341G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36032 AN: 151946 Hom.: 5503 Cov.: 33

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.0559

Gnomad SAS AF: 0.0793

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.238 AC: 36117 AN: 152062 Hom.: 5522 Cov.: 33 AF XY: 0.232 AC XY: 17219 AN XY: 74320

African (AFR) AF: 0.436 AC: 18057 AN: 41458

American (AMR) AF: 0.169 AC: 2576 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3468

East Asian (EAS) AF: 0.0558 AC: 289 AN: 5178

South Asian (SAS) AF: 0.0788 AC: 380 AN: 4822

European-Finnish (FIN) AF: 0.165 AC: 1746 AN: 10556

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11986 AN: 67986

Other (OTH) AF: 0.217 AC: 458 AN: 2110

Alfa AF: 0.219 Hom.: 605

Bravo AF: 0.245

Asia WGS AF: 0.115 AC: 398 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.23
DANN	Benign	0.28
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9808557; hg19: chr2-189149853;