chr6-133564585-G-T

Variant names:

• chr6-133564585-G-T
• rs6569884
• ENST00000607033.5:n.682+3605C>A

Variant summary

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

The ENST00000607033.5(TARID):​n.682+3605C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.496 in 151,950 control chromosomes in the GnomAD database, including 22,565 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 0.50 (22565 hom., cov: 32)
• Consequence: TARID ENST00000607033.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424
• Publications: 3 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 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.706+3605C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TARID	ENST00000607033.5	TSL:1	n.682+3605C>A		intron	N/A
	TARID	ENST00000419627.2	TSL:5	n.750+3605C>A		intron	N/A
	TARID	ENST00000606292.5	TSL:4	n.271+3605C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75285 AN: 151832 Hom.: 22532 Cov.: 32

Gnomad AFR AF: 0.851

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.496 AC: 75366 AN: 151950 Hom.: 22565 Cov.: 32 AF XY: 0.489 AC XY: 36296 AN XY: 74242

African (AFR) AF: 0.851 AC: 35349 AN: 41530

American (AMR) AF: 0.372 AC: 5671 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1594 AN: 3458

East Asian (EAS) AF: 0.348 AC: 1796 AN: 5168

South Asian (SAS) AF: 0.450 AC: 2165 AN: 4814

European-Finnish (FIN) AF: 0.270 AC: 2838 AN: 10512

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24338 AN: 67902

Other (OTH) AF: 0.483 AC: 1019 AN: 2108

Alfa AF: 0.403 Hom.: 22070

Bravo AF: 0.519

Asia WGS AF: 0.453 AC: 1573 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.17
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs6569884; hg19: chr6-133885723;