chr6-133546664-G-A

Variant names:

• chr6-133546664-G-A
• rs9375969
• ENST00000607033.5:n.683-9306C>T

Variant summary

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

The ENST00000607033.5(TARID):​n.683-9306C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,168 control chromosomes in the GnomAD database, including 2,841 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 0.17 (2841 hom., cov: 33)
• Consequence: TARID ENST00000607033.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 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.707-9306C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TARID	ENST00000607033.5	TSL:1	n.683-9306C>T		intron	N/A
	TARID	ENST00000419627.2	TSL:5	n.751-8472C>T		intron	N/A
	TARID	ENST00000606292.5	TSL:4	n.272-8472C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26537 AN: 152052 Hom.: 2846 Cov.: 33

Gnomad AFR AF: 0.0516

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.250

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.174 AC: 26524 AN: 152168 Hom.: 2841 Cov.: 33 AF XY: 0.176 AC XY: 13104 AN XY: 74380

African (AFR) AF: 0.0514 AC: 2133 AN: 41518

American (AMR) AF: 0.188 AC: 2875 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 637 AN: 3470

East Asian (EAS) AF: 0.249 AC: 1289 AN: 5178

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4814

European-Finnish (FIN) AF: 0.209 AC: 2206 AN: 10578

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15153 AN: 68006

Other (OTH) AF: 0.181 AC: 382 AN: 2108

Alfa AF: 0.187 Hom.: 3253

Bravo AF: 0.165

Asia WGS AF: 0.273 AC: 950 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.54
DANN	Benign	0.83
PhyloP100		-1.1

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: rs9375969;

hg19: chr6-133867802;