2-58906378-C-T

Variant names:

• chr2-58906378-C-T
• rs1861100
• ENST00000422723.5:n.503-18167C>T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000427421.5(LINC01122):​n.425-6341C>T variant causes a intron change. The variant allele was found at a frequency of 0.693 in 151,880 control chromosomes in the GnomAD database, including 36,923 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 0.69 (36923 hom., cov: 32)
• Consequence: LINC01122 ENST00000427421.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.85

Genes affected

LINC01122 (HGNC:49267): (long intergenic non-protein coding RNA 1122)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.27).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01122	NR_033873.1	n.425-6341C>T		intron_variant	Intron 3 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01122	ENST00000422723.5	n.503-18167C>T		intron_variant	Intron 4 of 5	3
LINC01122	ENST00000422793.3	n.361-18167C>T		intron_variant	Intron 4 of 6	5
LINC01122	ENST00000427421.5	n.425-6341C>T		intron_variant	Intron 3 of 13	2

Frequencies

GnomAD3 genomes AF: 0.693 AC: 105179 AN: 151762 Hom.: 36932 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.703

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.693 AC: 105188 AN: 151880 Hom.: 36923 Cov.: 32 AF XY: 0.695 AC XY: 51619 AN XY: 74230

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.722

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.703

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.723

Alfa AF: 0.729 Hom.: 39505

Bravo AF: 0.685

Asia WGS AF: 0.738 AC: 2567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	23
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1861100; hg19: chr2-59133513;