ENST00000607033.5:n.624-809T>C

Variant names:

• chr6-133569057-A-G
• rs10046269
• ENST00000607033.5:n.624-809T>C

Variant summary

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

The ENST00000607033.5(TARID):​n.624-809T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 152,122 control chromosomes in the GnomAD database, including 4,402 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 0.13 (4402 hom., cov: 32)
• Consequence: TARID ENST00000607033.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.66
• Publications: 2 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=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TARID	NR_109982.1		n.648-809T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TARID	ENST00000607033.5	TSL:1	n.624-809T>C		intron	N/A
	TARID	ENST00000419627.2	TSL:5	n.692-809T>C		intron	N/A
	TARID	ENST00000606292.5	TSL:4	n.213-809T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20309 AN: 152004 Hom.: 4378 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0654

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.0563

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.000753

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.00229

Gnomad OTH AF: 0.109

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.134 AC: 20384 AN: 152122 Hom.: 4402 Cov.: 32 AF XY: 0.130 AC XY: 9683 AN XY: 74392

African (AFR) AF: 0.450 AC: 18650 AN: 41414

American (AMR) AF: 0.0653 AC: 998 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00461 AC: 16 AN: 3472

East Asian (EAS) AF: 0.0566 AC: 293 AN: 5178

South Asian (SAS) AF: 0.00249 AC: 12 AN: 4828

European-Finnish (FIN) AF: 0.000753 AC: 8 AN: 10620

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.00229 AC: 156 AN: 68006

Other (OTH) AF: 0.107 AC: 227 AN: 2112

Alfa AF: 0.0894 Hom.: 3990

Bravo AF: 0.154

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	20
DANN	Benign	0.76
PhyloP100		2.7

Splicing

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

Other links and lift over

dbSNP: rs10046269; hg19: chr6-133890195;