ENST00000434418.2:n.496+104029A>G

Variant names:

• chr2-187931567-T-C
• rs10181512
• ENST00000434418.2:n.496+104029A>G

Variant summary

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

The ENST00000434418.2(LINC01090):​n.496+104029A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,884 control chromosomes in the GnomAD database, including 25,768 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 0.58 (25768 hom., cov: 31)
• Consequence: LINC01090 ENST00000434418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 1 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=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.676 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
LINC01090	ENST00000434418.2	n.496+104029A>G		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88065 AN: 151766 Hom.: 25743 Cov.: 31

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.648

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.580 AC: 88137 AN: 151884 Hom.: 25768 Cov.: 31 AF XY: 0.581 AC XY: 43082 AN XY: 74210

African (AFR) AF: 0.637 AC: 26392 AN: 41400

American (AMR) AF: 0.565 AC: 8626 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1835 AN: 3472

East Asian (EAS) AF: 0.648 AC: 3335 AN: 5148

South Asian (SAS) AF: 0.695 AC: 3344 AN: 4810

European-Finnish (FIN) AF: 0.528 AC: 5564 AN: 10542

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37178 AN: 67930

Other (OTH) AF: 0.550 AC: 1160 AN: 2110

Alfa AF: 0.564 Hom.: 65098

Bravo AF: 0.589

Asia WGS AF: 0.706 AC: 2456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs10181512; hg19: chr2-188796294;