Genetic Variant ENST00000737788.1:n.191-23983C>T (chr6-40313134-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000737788.1(TDRG1):n.191-23983C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,136 control chromosomes in the GnomAD database, including 4,140 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 0.22 ( 4140 hom., cov: 33)

Consequence

TDRG1
ENST00000737788.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.117

Publications

1 publications found

Variant links:

Genes affected

TDRG1 (HGNC:43642): (testis development related 1) Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

TDRG1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TDRG1	ENST00000737788.1 link	n.191-23983C>T		intron_variant	Intron 1 of 2
TDRG1	ENST00000737789.1 link	n.193+27262C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.221

AC:

33662

AN:

152018

Hom.:

4140

Cov.:

show subpopulations

Gnomad AFR

AF:

0.126

Gnomad AMI

AF:

0.289

Gnomad AMR

AF:

0.194

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.233

Gnomad SAS

AF:

0.406

Gnomad FIN

AF:

0.230

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.264

Gnomad OTH

AF:

0.240

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

GnomAD4 genome

AF:

0.221

AC:

33659

AN:

152136

Hom.:

4140

Cov.:

AF XY:

0.224

AC XY:

16626

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.126

AC:

5230

AN:

41526

American (AMR)

AF:

0.193

AC:

2958

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.308

AC:

1069

AN:

3468

East Asian (EAS)

AF:

0.232

AC:

1202

AN:

5178

South Asian (SAS)

AF:

0.406

AC:

1955

AN:

4814

European-Finnish (FIN)

AF:

0.230

AC:

2428

AN:

10564

Middle Eastern (MID)

AF:

0.224

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.264

AC:

17979

AN:

67978

Other (OTH)

AF:

0.240

AC:

508

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1335

2670

4005

5340

6675

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

384

768

1152

1536

1920

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.238

Hom.:

814

Bravo

AF:

0.208

Asia WGS

AF:

0.318

AC:

1108

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.0

(source)

DANN

Benign

0.52

PhyloP100

0.12

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over