2-120465698-C-T

Position:

• chr2-120465698-C-T

Variant summary

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

The NR_027181.1(LINC01101):​n.652G>A 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 0.105 in 456,696 control chromosomes in the GnomAD database, including 3,994 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 0.11 (1242 hom., cov: 33)
  • Exomes 𝑓: 0.10 (2752 hom.)
• Consequence: LINC01101 NR_027181.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327

Genes affected

LINC01101 (HGNC:25923): (long intergenic non-protein coding RNA 1101)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01101	NR_027181.1	n.652G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01101	ENST00000622953.1	n.521G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16062 AN: 152166 Hom.: 1239 Cov.: 33

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0804

Gnomad ASJ AF: 0.0827

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.0445

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0565

Gnomad OTH AF: 0.0917

GnomAD3 exomes AF: 0.109 AC: 14967 AN: 137004 Hom.: 1279 AF XY: 0.116 AC XY: 8620 AN XY: 74398

Gnomad AFR exome AF: 0.197

Gnomad AMR exome AF: 0.0781

Gnomad ASJ exome AF: 0.0859

Gnomad EAS exome AF: 0.176

Gnomad SAS exome AF: 0.243

Gnomad FIN exome AF: 0.0423

Gnomad NFE exome AF: 0.0573

Gnomad OTH exome AF: 0.0863

GnomAD4 exome AF: 0.104 AC: 31810 AN: 304410 Hom.: 2752 Cov.: 0 AF XY: 0.117 AC XY: 20258 AN XY: 173342

Gnomad4 AFR exome AF: 0.191

Gnomad4 AMR exome AF: 0.0790

Gnomad4 ASJ exome AF: 0.0876

Gnomad4 EAS exome AF: 0.176

Gnomad4 SAS exome AF: 0.238

Gnomad4 FIN exome AF: 0.0380

Gnomad4 NFE exome AF: 0.0574

Gnomad4 OTH exome AF: 0.0976

GnomAD4 genome AF: 0.106 AC: 16103 AN: 152286 Hom.: 1242 Cov.: 33 AF XY: 0.108 AC XY: 8063 AN XY: 74460

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.0811

Gnomad4 ASJ AF: 0.0827

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.248

Gnomad4 FIN AF: 0.0445

Gnomad4 NFE AF: 0.0565

Gnomad4 OTH AF: 0.0950

Alfa AF: 0.0687 Hom.: 501

Bravo AF: 0.108

Asia WGS AF: 0.262 AC: 912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	3.8
DANN	Benign	0.56

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17050160; hg19: chr2-121223274;