2-46782579-G-A

Variant names:

• chr2-46782579-G-A
• rs11125090
• ENST00000650611.2:n.173-14740G>A

Variant summary

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

The ENST00000650611.2(LINC01118):​n.173-14740G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0487 in 152,292 control chromosomes in the GnomAD database, including 344 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 0.049 (344 hom., cov: 32)
• Consequence: LINC01118 ENST00000650611.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.278
• Publications: 4 publications found

Genes affected

LINC01118 (HGNC:49261): (long intergenic non-protein coding RNA 1118)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01118	ENST00000650611.2	n.173-14740G>A		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.0488 AC: 7420 AN: 152174 Hom.: 345 Cov.: 32

Gnomad AFR AF: 0.0662

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0227

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.0782

Gnomad FIN AF: 0.0396

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0279

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0487 AC: 7416 AN: 152292 Hom.: 344 Cov.: 32 AF XY: 0.0502 AC XY: 3740 AN XY: 74460

African (AFR) AF: 0.0663 AC: 2757 AN: 41556

American (AMR) AF: 0.0227 AC: 347 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0406 AC: 141 AN: 3472

East Asian (EAS) AF: 0.265 AC: 1371 AN: 5172

South Asian (SAS) AF: 0.0783 AC: 378 AN: 4830

European-Finnish (FIN) AF: 0.0396 AC: 420 AN: 10614

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0279 AC: 1898 AN: 68030

Other (OTH) AF: 0.0421 AC: 89 AN: 2114

Alfa AF: 0.0302 Hom.: 123

Bravo AF: 0.0489

Asia WGS AF: 0.135 AC: 469 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs11125090; hg19: chr2-47009718;