dbSNP rs9375969: TARID:n.683-9306C>T (chr6-133546664-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000607033.5(TARID):n.683-9306C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 152,168 control chromosomes in the GnomAD database, including 2,841 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 0.17 ( 2841 hom., cov: 33)

Consequence

TARID
ENST00000607033.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.11

Variant links:

Genes affected

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

TARID links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TARID	NR_109982.1 link	n.707-9306C>T		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TARID	ENST00000607033.5 link	n.683-9306C>T	intron_variant	Intron 5 of 8	1
TARID	ENST00000606292.5 link	n.272-8472C>T	intron_variant	Intron 2 of 3	4
TARID	ENST00000606544.5 link	n.679-9306C>T	intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes

AF:

0.175

AC:

26537

AN:

152052

Hom.:

2846

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0516

Gnomad AMI

AF:

0.279

Gnomad AMR

AF:

0.188

Gnomad ASJ

AF:

0.184

Gnomad EAS

AF:

0.250

Gnomad SAS

AF:

0.320

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.223

Gnomad OTH

AF:

0.182

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

GnomAD4 genome

AF:

0.174

AC:

26524

AN:

152168

Hom.:

2841

Cov.:

AF XY:

0.176

AC XY:

13104

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.0514

Gnomad4 AMR

AF:

0.188

Gnomad4 ASJ

AF:

0.184

Gnomad4 EAS

AF:

0.249

Gnomad4 SAS

AF:

0.321

Gnomad4 FIN

AF:

0.209

Gnomad4 NFE

AF:

0.223

Gnomad4 OTH

AF:

0.181

Alfa

AF:

0.201

Hom.:

1379

Bravo

AF:

0.165

Asia WGS

AF:

0.273

AC:

950

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.54

DANN

Benign

0.83

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over