2-46789331-G-T

Variant names:

• chr2-46789331-G-T
• rs12615264
• ENST00000650611.1:n.173-7988G>T

Variant summary

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

The ENST00000650611.1(LINC01118):​n.173-7988G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0486 in 152,220 control chromosomes in the GnomAD database, including 332 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 (332 hom., cov: 33)
• Consequence: LINC01118 ENST00000650611.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.251 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.173-7988G>T		intron_variant	Intron 1 of 7

Frequencies

GnomAD3 genomes AF: 0.0486 AC: 7399 AN: 152102 Hom.: 333 Cov.: 33

Gnomad AFR AF: 0.0662

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0225

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.0772

Gnomad FIN AF: 0.0395

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: 0.0486 AC: 7392 AN: 152220 Hom.: 332 Cov.: 33 AF XY: 0.0502 AC XY: 3736 AN XY: 74432

Gnomad4 AFR AF: 0.0662

Gnomad4 AMR AF: 0.0225

Gnomad4 ASJ AF: 0.0406

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.0773

Gnomad4 FIN AF: 0.0395

Gnomad4 NFE AF: 0.0280

Gnomad4 OTH AF: 0.0416

Alfa AF: 0.00851 Hom.: 2

Bravo AF: 0.0488

Asia WGS AF: 0.135 AC: 466 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12615264; hg19: chr2-47016470;