rs6569884

chr6-133564585-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.706+3605C>A 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 0.496 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 NR_109982.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.424

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TARID	NR_109982.1	n.706+3605C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TARID	ENST00000607033.5	n.682+3605C>A		intron_variant, non_coding_transcript_variant		1

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

Gnomad4 AFR AF: 0.851

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.461

Gnomad4 EAS AF: 0.348

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.270

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.483

Alfa AF: 0.390 Hom.: 16005

Bravo AF: 0.519

Asia WGS AF: 0.453 AC: 1573 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6569884; hg19: chr6-133885723;