2-120465698-C-T

Variant names:

• chr2-120465698-C-T
• rs17050160
• ENST00000622953.1:n.521G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000622953.1(LINC01101):​n.521G>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 ENST00000622953.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.327
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01101	NR_027181.1	n.652G>A		non_coding_transcript_exon_variant	Exon 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01101	ENST00000622953.1	n.521G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC01101	ENST00000740733.1	n.314+517G>A		intron_variant	Intron 1 of 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

GnomAD2 exomes AF: 0.109 AC: 14967 AN: 137004 AF XY: 0.116

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 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

African (AFR) AF: 0.191 AC: 1648 AN: 8628

American (AMR) AF: 0.0790 AC: 2154 AN: 27282

Ashkenazi Jewish (ASJ) AF: 0.0876 AC: 945 AN: 10790

East Asian (EAS) AF: 0.176 AC: 1622 AN: 9210

South Asian (SAS) AF: 0.238 AC: 14204 AN: 59744

European-Finnish (FIN) AF: 0.0380 AC: 486 AN: 12792

Middle Eastern (MID) AF: 0.0845 AC: 235 AN: 2782

European-Non Finnish (NFE) AF: 0.0574 AC: 9127 AN: 158944

Other (OTH) AF: 0.0976 AC: 1389 AN: 14238

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

African (AFR) AF: 0.190 AC: 7909 AN: 41538

American (AMR) AF: 0.0811 AC: 1241 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0827 AC: 287 AN: 3472

East Asian (EAS) AF: 0.172 AC: 892 AN: 5186

South Asian (SAS) AF: 0.248 AC: 1195 AN: 4820

European-Finnish (FIN) AF: 0.0445 AC: 473 AN: 10620

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0565 AC: 3843 AN: 68026

Other (OTH) AF: 0.0950 AC: 201 AN: 2116

Alfa AF: 0.0734 Hom.: 1527

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
PhyloP100		0.33
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17050160; hg19: chr2-121223274;