rs9808557

chr2-188285126-C-T

Variant summary

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

The NR_126396.1(LINC01090):n.225+2341G>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 0.238 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 NR_126396.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

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=-0.94).
• 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/exons	MANE	UniProt
LINC01090	NR_126396.1	n.225+2341G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01090	ENST00000434418.2	n.225+2341G>A		intron_variant, non_coding_transcript_variant		5
LINC01090	ENST00000415357.1	n.168+2341G>A		intron_variant, non_coding_transcript_variant		3
LINC01090	ENST00000632331.1	n.81-95998G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.436

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.0558

Gnomad4 SAS AF: 0.0788

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.217

Alfa AF: 0.211 Hom.: 526

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9808557; hg19: chr2-189149853;