rs12742923

Variant names:

• chr1-83024161-C-T
• rs12742923
• ENST00000452901.5:n.1056+26572C>T

Variant summary

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

The ENST00000452901.5(LINC01362):​n.1056+26572C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,170 control chromosomes in the GnomAD database, including 1,447 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 0.13 (1447 hom., cov: 32)
• Consequence: LINC01362 ENST00000452901.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 7 publications found

Genes affected

LINC01362 (HGNC:50596): (long intergenic non-protein coding RNA 1362)

LINC01725 (HGNC:52513): (long intergenic non-protein coding RNA 1725)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000452901.5. 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
	LINC01362	NR_147074.1		n.1056+26572C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01362	ENST00000452901.5	TSL:1	n.1056+26572C>T		intron	N/A
	LINC01362	ENST00000659533.1		n.605+26572C>T		intron	N/A
	LINC01362	ENST00000669455.1		n.529+26572C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19650 AN: 152052 Hom.: 1440 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.00444

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.129 AC: 19675 AN: 152170 Hom.: 1447 Cov.: 32 AF XY: 0.131 AC XY: 9728 AN XY: 74402

African (AFR) AF: 0.126 AC: 5216 AN: 41524

American (AMR) AF: 0.111 AC: 1703 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 488 AN: 3468

East Asian (EAS) AF: 0.00445 AC: 23 AN: 5172

South Asian (SAS) AF: 0.265 AC: 1280 AN: 4822

European-Finnish (FIN) AF: 0.111 AC: 1178 AN: 10588

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9286 AN: 67998

Other (OTH) AF: 0.121 AC: 256 AN: 2114

Alfa AF: 0.132 Hom.: 2425

Bravo AF: 0.123

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.63
PhyloP100		-0.35

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12742923;

hg19: chr1-83489844;