rs10046269

chr6-133569057-A-G

Variant summary

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

The NR_109982.1(TARID):n.648-809T>C 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 0.134 in 152,122 control chromosomes in the GnomAD database, including 4,402 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 0.13 (4402 hom., cov: 32)
• Consequence: TARID NR_109982.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.66

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=-0.61).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TARID	NR_109982.1	n.648-809T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TARID	ENST00000607033.5	n.624-809T>C		intron_variant, non_coding_transcript_variant		1
TARID	ENST00000606292.5	n.213-809T>C		intron_variant, non_coding_transcript_variant		4
TARID	ENST00000606544.5	n.624-809T>C		intron_variant, non_coding_transcript_variant		5
TARID	ENST00000607573.5	n.344-809T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20309 AN: 152004 Hom.: 4378 Cov.: 32

Gnomad AFR AF: 0.450

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0654

Gnomad ASJ AF: 0.00461

Gnomad EAS AF: 0.0563

Gnomad SAS AF: 0.00269

Gnomad FIN AF: 0.000753

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.00229

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.134 AC: 20384 AN: 152122 Hom.: 4402 Cov.: 32 AF XY: 0.130 AC XY: 9683 AN XY: 74392

Gnomad4 AFR AF: 0.450

Gnomad4 AMR AF: 0.0653

Gnomad4 ASJ AF: 0.00461

Gnomad4 EAS AF: 0.0566

Gnomad4 SAS AF: 0.00249

Gnomad4 FIN AF: 0.000753

Gnomad4 NFE AF: 0.00229

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0411 Hom.: 1108

Bravo AF: 0.154

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
Cadd	Benign	20
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10046269; hg19: chr6-133890195;