chr12-127898157-C-T

Variant names:

• chr12-127898157-C-T
• rs1463669
• ENST00000614177.2:n.1511C>T

Variant summary

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

The ENST00000614177.2(LINC02393):​n.1511C>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 0.722 in 152,130 control chromosomes in the GnomAD database, including 44,283 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 0.72 (44275 hom., cov: 33)
  • Exomes 𝑓: 0.90 (8 hom.)
• Consequence: LINC02393 ENST00000614177.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• Publications: 5 publications found

Genes affected

LINC02393 (HGNC:53320): (long intergenic non-protein coding RNA 2393)

LINC00508 (HGNC:43559): (long intergenic non-protein coding RNA 508)

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 = 0.888 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000614177.2. 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
	LINC02393	NR_033987.1		n.1538C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC00508	NR_126452.2		n.312-13052G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02393	ENST00000614177.2	TSL:2	n.1511C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC02393	ENST00000662498.1		n.1445C>T		non_coding_transcript_exon	Exon 2 of 2
	LINC00508	ENST00000741352.1		n.317-36301G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.723 AC: 109839 AN: 151994 Hom.: 44259 Cov.: 33

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.861

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.765

GnomAD4 exome AF: 0.900 AC: 18 AN: 20 Hom.: 8 Cov.: 0 AF XY: 0.889 AC XY: 16 AN XY: 18

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 12 AN: 12

Other (OTH) AF: 0.667 AC: 4 AN: 6

GnomAD4 genome AF: 0.722 AC: 109892 AN: 152110 Hom.: 44275 Cov.: 33 AF XY: 0.727 AC XY: 54030 AN XY: 74362

African (AFR) AF: 0.344 AC: 14254 AN: 41468

American (AMR) AF: 0.840 AC: 12845 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3261 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2606 AN: 5142

South Asian (SAS) AF: 0.910 AC: 4380 AN: 4812

European-Finnish (FIN) AF: 0.861 AC: 9127 AN: 10596

Middle Eastern (MID) AF: 0.829 AC: 242 AN: 292

European-Non Finnish (NFE) AF: 0.893 AC: 60734 AN: 68014

Other (OTH) AF: 0.768 AC: 1623 AN: 2114

Alfa AF: 0.836 Hom.: 140332

Bravo AF: 0.700

Asia WGS AF: 0.689 AC: 2396 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	3.8
DANN	Benign	0.52
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1463669; hg19: chr12-128382702;