2-46785687-G-T

Variant names:

• chr2-46785687-G-T
• rs11682595
• ENST00000650611.1:n.173-11632G>T

Variant summary

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

The ENST00000650611.1(LINC01118):​n.173-11632G>T 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 152,200 control chromosomes in the GnomAD database, including 338 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 (338 hom., cov: 32)
• Consequence: LINC01118 ENST00000650611.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.522

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.254 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	ENST00000650611.1	n.173-11632G>T		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.0488 AC: 7418 AN: 152082 Hom.: 339 Cov.: 32

Gnomad AFR AF: 0.0663

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0225

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.0397

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0280

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0487 AC: 7414 AN: 152200 Hom.: 338 Cov.: 32 AF XY: 0.0503 AC XY: 3746 AN XY: 74414

Gnomad4 AFR AF: 0.0664

Gnomad4 AMR AF: 0.0224

Gnomad4 ASJ AF: 0.0407

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.0777

Gnomad4 FIN AF: 0.0397

Gnomad4 NFE AF: 0.0279

Gnomad4 OTH AF: 0.0417

Alfa AF: 0.0205 Hom.: 13

Bravo AF: 0.0490

Asia WGS AF: 0.135 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11682595; hg19: chr2-47012826;