6-133820171-C-T

Position:

• chr6-133820171-C-T

Variant summary

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

The NR_109982.1(TARID):​n.478+25706G>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 0.232 in 152,116 control chromosomes in the GnomAD database, including 4,827 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 0.23 (4827 hom., cov: 32)
• Consequence: TARID NR_109982.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TARID	NR_109982.1	n.478+25706G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TARID	ENST00000607033.5	n.454+25706G>A		intron_variant, non_coding_transcript_variant		1
TARID	ENST00000419627.1	n.75+25706G>A		intron_variant, non_coding_transcript_variant		5
TARID	ENST00000606544.5	n.454+25706G>A		intron_variant, non_coding_transcript_variant		5
TARID	ENST00000607573.5	n.251-51248G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35273 AN: 151998 Hom.: 4822 Cov.: 32

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.311

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.232 AC: 35283 AN: 152116 Hom.: 4827 Cov.: 32 AF XY: 0.228 AC XY: 16957 AN XY: 74360

Gnomad4 AFR AF: 0.0958

Gnomad4 AMR AF: 0.185

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.311

Gnomad4 OTH AF: 0.206

Alfa AF: 0.296 Hom.: 12988

Bravo AF: 0.221

Asia WGS AF: 0.268 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1041714; hg19: chr6-134141309;