rs969282

Variant names:

• chr6-133883954-G-A
• rs969282
• ENST00000607033.5:n.379+4650C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-133883954-G-A
• chr6-133883954-G-T

Variant summary

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

The ENST00000607033.5(TARID):​n.379+4650C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.633 in 151,928 control chromosomes in the GnomAD database, including 31,202 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 0.63 (31202 hom., cov: 31)
• Consequence: TARID ENST00000607033.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TARID	NR_109982.1	n.403+4650C>T		intron_variant	Intron 1 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TARID	ENST00000607033.5	n.379+4650C>T		intron_variant	Intron 1 of 8	1
TARID	ENST00000419627.2	n.447+4650C>T		intron_variant	Intron 1 of 5	5
TARID	ENST00000606544.5	n.379+4650C>T		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95993 AN: 151810 Hom.: 31149 Cov.: 31

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.594

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.633 AC: 96099 AN: 151928 Hom.: 31202 Cov.: 31 AF XY: 0.637 AC XY: 47282 AN XY: 74254

African (AFR) AF: 0.797 AC: 33039 AN: 41456

American (AMR) AF: 0.615 AC: 9397 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.594 AC: 2057 AN: 3464

East Asian (EAS) AF: 0.552 AC: 2844 AN: 5154

South Asian (SAS) AF: 0.606 AC: 2912 AN: 4804

European-Finnish (FIN) AF: 0.639 AC: 6729 AN: 10538

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.547 AC: 37175 AN: 67922

Other (OTH) AF: 0.631 AC: 1331 AN: 2108

Alfa AF: 0.571 Hom.: 49896

Bravo AF: 0.640

Asia WGS AF: 0.633 AC: 2199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.81
DANN	Benign	0.74
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs969282; hg19: chr6-134205092;