rs12562034

Variant names:

• chr1-833068-G-A
• rs12562034
• ENST00000415295.1:n.73+1391G>A

Variant summary

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

The ENST00000415295.1(LINC01128):​n.73+1391G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 151,546 control chromosomes in the GnomAD database, including 1,605 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 0.12 (1605 hom., cov: 32)
• Consequence: LINC01128 ENST00000415295.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 8 publications found

Genes affected

LINC01128 (HGNC:49377): (long intergenic non-protein coding RNA 1128)

ENSG00000297178 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000415295.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01128	NR_047519.1		n.287+3964G>A		intron	N/A
	LINC01128	NR_047521.1		n.287+3964G>A		intron	N/A
	LINC01128	NR_047523.1		n.287+3964G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01128	ENST00000415295.1	TSL:1	n.73+1391G>A		intron	N/A
	LINC01128	ENST00000445118.7	TSL:1	n.280+3964G>A		intron	N/A
	LINC01128	ENST00000449005.8	TSL:1	n.268+3964G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17892 AN: 151440 Hom.: 1596 Cov.: 32

Gnomad AFR AF: 0.0840

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.118 AC: 17920 AN: 151546 Hom.: 1605 Cov.: 32 AF XY: 0.124 AC XY: 9179 AN XY: 74010

African (AFR) AF: 0.0842 AC: 3484 AN: 41402

American (AMR) AF: 0.102 AC: 1533 AN: 15014

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 471 AN: 3468

East Asian (EAS) AF: 0.405 AC: 2038 AN: 5032

South Asian (SAS) AF: 0.285 AC: 1362 AN: 4778

European-Finnish (FIN) AF: 0.118 AC: 1251 AN: 10558

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7362 AN: 67992

Other (OTH) AF: 0.111 AC: 233 AN: 2096

Alfa AF: 0.109 Hom.: 1656

Bravo AF: 0.113

Asia WGS AF: 0.283 AC: 964 AN: 3412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.69
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs12562034; hg19: chr1-768448;