6-46686052-A-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000422284.7(TDRD6-AS1):​n.270+1548T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)

Consequence

TDRD6-AS1
ENST00000422284.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.36

Publications

10 publications found
Variant links:
Genes affected
TDRD6-AS1 (HGNC:56119): (TDRD6 and SLC25A27 antisense RNA 1)
TDRD6 (HGNC:21339): (tudor domain containing 6) This gene encodes a tudor domain-containing protein and component of the chromatoid body, a type of ribonucleoprotein granule present in male germ cells. Studies in rodents have demonstrated a role for the encoded protein in spermiogenesis and the nonsense mediated decay (NMD) pathway. This protein is a major autoantigen in human patients with autoimmune polyendocrine syndrome type 1 (APS1). [provided by RefSeq, Oct 2016]
TDRD6 Gene-Disease associations (from GenCC):
  • male infertility with azoospermia or oligozoospermia due to single gene mutation
    Inheritance: AR Classification: MODERATE Submitted by: King Faisal Specialist Hospital and Research Center
  • schizophrenia
    Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
  • oligospermia
    Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TDRD6-AS1NR_134642.1 linkn.234+1548T>G intron_variant Intron 1 of 1
TDRD6-AS1NR_134643.1 linkn.232+1882T>G intron_variant Intron 1 of 1
TDRD6-AS1NR_134644.1 linkn.159+1623T>G intron_variant Intron 1 of 1
TDRD6NR_144468.2 linkn.1372+4413A>C intron_variant Intron 1 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TDRD6-AS1ENST00000422284.7 linkn.270+1548T>G intron_variant Intron 1 of 1 2
TDRD6-AS1ENST00000434329.3 linkn.362+1882T>G intron_variant Intron 1 of 1 3
TDRD6-AS1ENST00000571590.6 linkn.199+1623T>G intron_variant Intron 1 of 1 3
TDRD6-AS1ENST00000734840.1 linkn.401+1398T>G intron_variant Intron 1 of 1

Frequencies

GnomAD3 genomes
Cov.:
30
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.46
DANN
Benign
0.59
PhyloP100
-1.4

Splicing

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

Publications

Other links and lift over

dbSNP: rs9472819; hg19: chr6-46653789; API