chr12-127897995-T-G

Variant names:

• chr12-127897995-T-G
• rs1463670
• ENST00000614177.2:n.1349T>G

Variant summary

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

The ENST00000614177.2(LINC02393):​n.1349T>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 0.215 in 152,134 control chromosomes in the GnomAD database, including 5,315 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 0.21 (5315 hom., cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC02393 ENST00000614177.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.99
• Publications: 2 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=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 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.1376T>G		non_coding_transcript_exon	Exon 3 of 3
	LINC00508	NR_126452.2		n.312-12890A>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02393	ENST00000614177.2	TSL:2	n.1349T>G		non_coding_transcript_exon	Exon 3 of 3
	LINC02393	ENST00000662498.1		n.1283T>G		non_coding_transcript_exon	Exon 2 of 2
	LINC00508	ENST00000741352.1		n.317-36139A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32672 AN: 152016 Hom.: 5311 Cov.: 33

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0574

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.0899

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.191

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 6 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 6

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.215 AC: 32705 AN: 152134 Hom.: 5315 Cov.: 33 AF XY: 0.214 AC XY: 15924 AN XY: 74392

African (AFR) AF: 0.439 AC: 18198 AN: 41486

American (AMR) AF: 0.138 AC: 2111 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0574 AC: 199 AN: 3466

East Asian (EAS) AF: 0.493 AC: 2546 AN: 5160

South Asian (SAS) AF: 0.0890 AC: 428 AN: 4810

European-Finnish (FIN) AF: 0.138 AC: 1468 AN: 10608

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7223 AN: 67998

Other (OTH) AF: 0.188 AC: 398 AN: 2114

Alfa AF: 0.0621 Hom.: 117

Bravo AF: 0.228

Asia WGS AF: 0.295 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.26
DANN	Benign	0.43
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs1463670; hg19: chr12-128382540;