12-127898157-C-T

Position:

• chr12-127898157-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC02393 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02393	NR_033987.1	n.1538C>T		non_coding_transcript_exon_variant	3/3
LINC00508	NR_126452.2	n.312-13052G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02393	ENST00000614177.2	n.1511C>T		non_coding_transcript_exon_variant	3/3	2
LINC02393	ENST00000662498.1	n.1445C>T		non_coding_transcript_exon_variant	2/2

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

Gnomad4 ASJ exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.667

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

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.910

Gnomad4 FIN AF: 0.861

Gnomad4 NFE AF: 0.893

Gnomad4 OTH AF: 0.768

Alfa AF: 0.867 Hom.: 93700

Bravo AF: 0.700

Asia WGS AF: 0.689 AC: 2396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1463669; hg19: chr12-128382702;