6-133837662-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027030.1(LINC01312):n.659T>C 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 0.277 in 152,194 control chromosomes in the GnomAD database, including 7,092 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 0.28 (7067 hom., cov: 30)
  • Exomes 𝑓: 0.32 (25 hom.)
• Consequence: LINC01312 NR_027030.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803

Genes affected

LINC01312 (HGNC:28525): (long intergenic non-protein coding RNA 1312)

TARID (HGNC:50506): (TCF21 antisense RNA inducing promoter demethylation)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01312	NR_027030.1	n.659T>C		non_coding_transcript_exon_variant	2/3
TARID	NR_109982.1	n.478+8215A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01312	ENST00000669925.1	n.627T>C		non_coding_transcript_exon_variant	2/4
TARID	ENST00000607033.5	n.454+8215A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.277 AC: 41969 AN: 151662 Hom.: 7063 Cov.: 30

Gnomad AFR AF: 0.0850

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.318

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.256

GnomAD4 exome AF: 0.321 AC: 133 AN: 414 Hom.: 25 Cov.: 0 AF XY: 0.304 AC XY: 73 AN XY: 240

Gnomad4 FIN exome AF: 0.323

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.277 AC: 41976 AN: 151780 Hom.: 7067 Cov.: 30 AF XY: 0.270 AC XY: 20006 AN XY: 74146

Gnomad4 AFR AF: 0.0849

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.318

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.277

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.256

Alfa AF: 0.359 Hom.: 22322

Bravo AF: 0.266

Asia WGS AF: 0.335 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	7.5
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1208285; hg19: chr6-134158800;