2-187736531-C-T

Variant names:

• chr2-187736531-C-T
• rs1520475
• ENST00000434418.2:n.497-23652G>A

Variant summary

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

The ENST00000434418.2(LINC01090):​n.497-23652G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 151,572 control chromosomes in the GnomAD database, including 35,679 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 0.66 (35679 hom., cov: 32)
• Consequence: LINC01090 ENST00000434418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.771 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.497-23652G>A		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.658 AC: 99625 AN: 151454 Hom.: 35671 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.780

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.657 AC: 99653 AN: 151572 Hom.: 35679 Cov.: 32 AF XY: 0.661 AC XY: 48978 AN XY: 74070

African (AFR) AF: 0.355 AC: 14652 AN: 41306

American (AMR) AF: 0.758 AC: 11528 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2611 AN: 3460

East Asian (EAS) AF: 0.780 AC: 4030 AN: 5164

South Asian (SAS) AF: 0.574 AC: 2760 AN: 4812

European-Finnish (FIN) AF: 0.863 AC: 9121 AN: 10572

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.777 AC: 52627 AN: 67744

Other (OTH) AF: 0.680 AC: 1430 AN: 2102

Alfa AF: 0.712 Hom.: 17486

Bravo AF: 0.639

Asia WGS AF: 0.626 AC: 2149 AN: 3438

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.61
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs1520475; hg19: chr2-188601258;