12-103559279-C-T

Variant names:

• chr12-103559279-C-T
• rs10861038
• ENST00000550185.5:n.2523C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000550185.5(LINC02401):​n.2523C>T 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 0.0000083 in 120,506 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0000083 (0 hom., cov: 30)
• Consequence: LINC02401 ENST00000550185.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37
• Publications: 4 publications found

Genes affected

LINC02401 (HGNC:53328): (long intergenic non-protein coding RNA 2401)

ENSG00000286197 (HGNC:):

C12orf42 (HGNC:24729): (chromosome 12 open reading frame 42)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000550185.5. 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
	LINC02401	NR_110103.1		n.2523C>T		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02401	ENST00000550185.5	TSL:1	n.2523C>T		non_coding_transcript_exon	Exon 5 of 5
	ENSG00000286197	ENST00000650784.1		n.204+4368G>A		intron	N/A
	LINC02401	ENST00000654623.1		n.845+1683C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.00000830 AC: 1 AN: 120506 Hom.: 0 Cov.: 30

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000204

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.00000830 AC: 1 AN: 120506 Hom.: 0 Cov.: 30 AF XY: 0.0000170 AC XY: 1 AN XY: 58698

African (AFR) AF: 0.00 AC: 0 AN: 38710

American (AMR) AF: 0.00 AC: 0 AN: 11466

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2998

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.00 AC: 0 AN: 4044

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6380

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 262

European-Non Finnish (NFE) AF: 0.0000204 AC: 1 AN: 49122

Other (OTH) AF: 0.00 AC: 0 AN: 1714

Alfa AF: 0.00 Hom.: 589

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	8.5
DANN	Benign	0.83
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs10861038; hg19: chr12-103953057;