chr2-131413315-G-A

Variant names:

• chr2-131413315-G-A
• rs7589111
• ENST00000846054.1:n.833-829G>A

Variant summary

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

The ENST00000846054.1(LINC01120):​n.833-829G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 152,038 control chromosomes in the GnomAD database, including 23,566 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 0.52 (23566 hom., cov: 32)
• Consequence: LINC01120 ENST00000846054.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 18 publications found

Genes affected

LINC01120 (HGNC:49265): (long intergenic non-protein coding RNA 1120)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846054.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01120	ENST00000846054.1		n.833-829G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79459 AN: 151922 Hom.: 23505 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.523 AC: 79576 AN: 152038 Hom.: 23566 Cov.: 32 AF XY: 0.528 AC XY: 39213 AN XY: 74306

African (AFR) AF: 0.783 AC: 32476 AN: 41484

American (AMR) AF: 0.606 AC: 9263 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1598 AN: 3472

East Asian (EAS) AF: 0.728 AC: 3759 AN: 5160

South Asian (SAS) AF: 0.429 AC: 2063 AN: 4808

European-Finnish (FIN) AF: 0.432 AC: 4561 AN: 10562

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24349 AN: 67942

Other (OTH) AF: 0.538 AC: 1138 AN: 2116

Alfa AF: 0.433 Hom.: 44635

Bravo AF: 0.555

Asia WGS AF: 0.609 AC: 2117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.77
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs7589111; hg19: chr2-132170888;