rs10496166

chr2-68836777-G-Achr2-68836777-G-C

Variant summary

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

The NR_183884.1(LINC01890):n.431C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,126 control chromosomes in the GnomAD database, including 5,746 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 0.25 (5746 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC01890 NR_183884.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424

Genes affected

LINC01890 (HGNC:52709): (long intergenic non-protein coding RNA 1890)

LINC01888 (HGNC:52707): (long intergenic non-protein coding RNA 1888)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01890	NR_183884.1	n.431C>T		non_coding_transcript_exon_variant	1/4
LINC01888	NR_183895.1	n.146-605G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01890	ENST00000655209.1	n.431C>T		non_coding_transcript_exon_variant	1/4
LINC01888	ENST00000655763.1	n.140-605G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37800 AN: 152008 Hom.: 5728 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.239

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 36 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 20

Gnomad4 AMR exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.249 AC: 37868 AN: 152126 Hom.: 5746 Cov.: 32 AF XY: 0.250 AC XY: 18614 AN XY: 74360

Gnomad4 AFR AF: 0.402

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.253

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.237

Alfa AF: 0.175 Hom.: 5998

Bravo AF: 0.265

Asia WGS AF: 0.348 AC: 1205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.57
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10496166; hg19: chr2-69063909;