chr6-46688821-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_001010870.3(TDRD6):c.693G>A(p.Pro231=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,612,486 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000031 ( 2 hom. )
Consequence
TDRD6
NM_001010870.3 synonymous
NM_001010870.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.331
Genes affected
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -7 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
?
Variant 6-46688821-G-A is Benign according to our data. Variant chr6-46688821-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2656623.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-0.331 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TDRD6 | NM_001010870.3 | c.693G>A | p.Pro231= | synonymous_variant | 1/4 | ENST00000316081.11 | |
TDRD6 | NM_001168359.2 | c.693G>A | p.Pro231= | synonymous_variant | 1/3 | ||
TDRD6 | NR_144468.2 | n.1373-7000G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TDRD6 | ENST00000316081.11 | c.693G>A | p.Pro231= | synonymous_variant | 1/4 | 1 | NM_001010870.3 | P2 | |
TDRD6 | ENST00000544460.5 | c.693G>A | p.Pro231= | synonymous_variant | 1/3 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152192Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000444 AC: 11AN: 247660Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134502
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GnomAD4 exome AF: 0.0000308 AC: 45AN: 1460176Hom.: 2 Cov.: 30 AF XY: 0.0000344 AC XY: 25AN XY: 726420
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | TDRD6: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Dann
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at