rs12623542

Variant names:

• chr2-241978628-T-G
• rs12623542
• ENST00000797012.1:n.2167T>G

Variant summary

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

The ENST00000797012.1(LINC01237):​n.2167T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,128 control chromosomes in the GnomAD database, including 17,509 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 0.46 (17509 hom., cov: 32)
• Consequence: LINC01237 ENST00000797012.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.189
• Publications: 8 publications found

Genes affected

LINC01237 (HGNC:49793): (long intergenic non-protein coding RNA 1237)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000797012.1. 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
	LINC01237	NR_110220.1		n.313+12581T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01237	ENST00000797012.1		n.2167T>G		non_coding_transcript_exon	Exon 6 of 6
	LINC01237	ENST00000415434.5	TSL:4	n.310+12581T>G		intron	N/A
	LINC01237	ENST00000685688.1		n.306-9070T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.459 AC: 69377 AN: 151010 Hom.: 17505 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.631

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.459 AC: 69405 AN: 151128 Hom.: 17509 Cov.: 32 AF XY: 0.464 AC XY: 34235 AN XY: 73846

African (AFR) AF: 0.357 AC: 14767 AN: 41346

American (AMR) AF: 0.379 AC: 5760 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1579 AN: 3432

East Asian (EAS) AF: 0.526 AC: 2718 AN: 5170

South Asian (SAS) AF: 0.512 AC: 2400 AN: 4688

European-Finnish (FIN) AF: 0.631 AC: 6619 AN: 10488

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34019 AN: 67506

Other (OTH) AF: 0.424 AC: 890 AN: 2098

Alfa AF: 0.466 Hom.: 3056

Bravo AF: 0.435

Asia WGS AF: 0.456 AC: 1585 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	5.7
DANN	Benign	0.92
PhyloP100		0.19

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: rs12623542;

hg19: chr2-242920779;