rs969282

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109982.1(TARID):​n.403+4650C>T variant causes a intron, non coding transcript 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 NR_109982.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387

Genes affected

TARID (HGNC:50506): (TCF21 antisense RNA inducing promoter demethylation)

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
TARID	NR_109982.1	n.403+4650C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TARID	ENST00000607033.5	n.379+4650C>T		intron_variant, non_coding_transcript_variant		1
TARID	ENST00000606544.5	n.379+4650C>T		intron_variant, non_coding_transcript_variant		5
TARID	ENST00000607573.5	n.250+7733C>T		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.797

Gnomad4 AMR AF: 0.615

Gnomad4 ASJ AF: 0.594

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.606

Gnomad4 FIN AF: 0.639

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.631

Alfa AF: 0.566 Hom.: 35343

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs969282; hg19: chr6-134205092;