6-133837662-T-C

Variant names:

• chr6-133837662-T-C
• rs1208285
• ENST00000456347.5:n.659T>C

Variant summary

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

The ENST00000456347.5(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 ENST00000456347.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.803
• Publications: 17 publications found

Genes affected

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

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456347.5. 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
	LINC01312	NR_027030.1		n.659T>C		non_coding_transcript_exon	Exon 2 of 3
	TARID	NR_109982.1		n.478+8215A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01312	ENST00000456347.5	TSL:1	n.659T>C		non_coding_transcript_exon	Exon 2 of 3
	TARID	ENST00000607033.5	TSL:1	n.454+8215A>G		intron	N/A
	LINC01312	ENST00000412745.2	TSL:3	n.128T>C		non_coding_transcript_exon	Exon 2 of 3

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

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: 0.323 AC: 131 AN: 406

Middle Eastern (MID) AC: 0 AN: 0

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

Other (OTH) AF: 0.333 AC: 2 AN: 6

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

African (AFR) AF: 0.0849 AC: 3518 AN: 41440

American (AMR) AF: 0.244 AC: 3719 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.318 AC: 1102 AN: 3464

East Asian (EAS) AF: 0.464 AC: 2370 AN: 5108

South Asian (SAS) AF: 0.294 AC: 1411 AN: 4792

European-Finnish (FIN) AF: 0.277 AC: 2906 AN: 10478

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25921 AN: 67934

Other (OTH) AF: 0.256 AC: 539 AN: 2106

Alfa AF: 0.341 Hom.: 32954

Bravo AF: 0.266

Asia WGS AF: 0.335 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.5
DANN	Benign	0.69
PhyloP100		0.80

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1208285;

hg19: chr6-134158800;