rs2028374

chr2-188118776-G-A

Variant summary

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

The NR_126396.1(LINC01090):n.380+46978C>T 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 0.743 in 152,048 control chromosomes in the GnomAD database, including 43,591 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 0.74 (43591 hom., cov: 32)
• Consequence: LINC01090 NR_126396.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.833

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01090	NR_126396.1	n.380+46978C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01090	ENST00000434418.2	n.380+46978C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.744 AC: 112978 AN: 151930 Hom.: 43587 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.817

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.757

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

GnomAD4 genome AF: 0.743 AC: 113017 AN: 152048 Hom.: 43591 Cov.: 32 AF XY: 0.750 AC XY: 55716 AN XY: 74328

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.870

Gnomad4 EAS AF: 0.943

Gnomad4 SAS AF: 0.894

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.754

Alfa AF: 0.802 Hom.: 21449

Bravo AF: 0.732

Asia WGS AF: 0.877 AC: 3049 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.30
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2028374; hg19: chr2-188983503;