6-133888699-T-C

Variant names:

• chr6-133888699-T-C
• rs2327429
• ENST00000607033.5:n.284A>G

Variant summary

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

The ENST00000607033.5(TARID):​n.284A>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 0.252 in 152,466 control chromosomes in the GnomAD database, including 5,869 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 0.25 (5860 hom., cov: 32)
  • Exomes 𝑓: 0.19 (9 hom.)
• Consequence: TARID ENST00000607033.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.245
• Publications: 30 publications found

Genes affected

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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607033.5. 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
	TARID	NR_109982.1		n.308A>G		non_coding_transcript_exon	Exon 1 of 9

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TARID	ENST00000607033.5	TSL:1	n.284A>G		non_coding_transcript_exon	Exon 1 of 9
	TARID	ENST00000607641.3	TSL:1	n.1630A>G		non_coding_transcript_exon	Exon 2 of 3
	TARID	ENST00000626104.2	TSL:1	n.1161A>G		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38375 AN: 151968 Hom.: 5848 Cov.: 32

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.285

GnomAD4 exome AF: 0.192 AC: 73 AN: 380 Hom.: 9 Cov.: 0 AF XY: 0.194 AC XY: 42 AN XY: 216

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AF: 0.250 AC: 7 AN: 28

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.250 AC: 2 AN: 8

European-Finnish (FIN) AF: 0.125 AC: 1 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.198 AC: 61 AN: 308

Other (OTH) AF: 0.100 AC: 2 AN: 20

GnomAD4 genome AF: 0.252 AC: 38397 AN: 152086 Hom.: 5860 Cov.: 32 AF XY: 0.258 AC XY: 19191 AN XY: 74326

African (AFR) AF: 0.0960 AC: 3987 AN: 41518

American (AMR) AF: 0.378 AC: 5778 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1264 AN: 3470

East Asian (EAS) AF: 0.521 AC: 2684 AN: 5150

South Asian (SAS) AF: 0.426 AC: 2044 AN: 4800

European-Finnish (FIN) AF: 0.235 AC: 2488 AN: 10590

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.283 AC: 19208 AN: 67966

Other (OTH) AF: 0.290 AC: 613 AN: 2114

Alfa AF: 0.284 Hom.: 26695

Bravo AF: 0.258

Asia WGS AF: 0.443 AC: 1538 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.5
DANN	Benign	0.45
PhyloP100		-0.24
PromoterAI		0.0072	Neutral

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: rs2327429;

hg19: chr6-134209837;

COSMIC: COSV52819505;