2-188018014-C-T

Position:

• chr2-188018014-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000434418.2(LINC01090):​n.496+17582G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0697 in 152,168 control chromosomes in the GnomAD database, including 500 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 0.070 (500 hom., cov: 32)
• Consequence: LINC01090 ENST00000434418.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01090	ENST00000434418.2	n.496+17582G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0696 AC: 10578 AN: 152050 Hom.: 497 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.0377

Gnomad SAS AF: 0.0338

Gnomad FIN AF: 0.0184

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0411

Gnomad OTH AF: 0.0761

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

GnomAD4 genome AF: 0.0697 AC: 10607 AN: 152168 Hom.: 500 Cov.: 32 AF XY: 0.0694 AC XY: 5164 AN XY: 74370

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.109

Gnomad4 ASJ AF: 0.0533

Gnomad4 EAS AF: 0.0372

Gnomad4 SAS AF: 0.0336

Gnomad4 FIN AF: 0.0184

Gnomad4 NFE AF: 0.0410

Gnomad4 OTH AF: 0.0777

Alfa AF: 0.0458 Hom.: 265

Bravo AF: 0.0809

Asia WGS AF: 0.0810 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10497689; hg19: chr2-188882741;