3-132447373-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_015268.4(DNAJC13):c.197C>T(p.Thr66Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000617 in 1,605,238 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015268.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJC13 | NM_015268.4 | c.197C>T | p.Thr66Met | missense_variant | Exon 4 of 56 | ENST00000260818.11 | NP_056083.3 | |
DNAJC13 | NM_001329126.2 | c.197C>T | p.Thr66Met | missense_variant | Exon 4 of 57 | NP_001316055.1 | ||
DNAJC13 | XM_047447819.1 | c.197C>T | p.Thr66Met | missense_variant | Exon 4 of 57 | XP_047303775.1 | ||
DNAJC13 | XM_047447820.1 | c.197C>T | p.Thr66Met | missense_variant | Exon 4 of 56 | XP_047303776.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAJC13 | ENST00000260818.11 | c.197C>T | p.Thr66Met | missense_variant | Exon 4 of 56 | 1 | NM_015268.4 | ENSP00000260818.6 | ||
DNAJC13 | ENST00000486798.5 | n.262C>T | non_coding_transcript_exon_variant | Exon 4 of 20 | 1 | |||||
DNAJC13 | ENST00000650455.1 | n.197C>T | non_coding_transcript_exon_variant | Exon 4 of 57 | ENSP00000496825.1 |
Frequencies
GnomAD3 genomes AF: 0.0000725 AC: 11AN: 151716Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000328 AC: 8AN: 243804Hom.: 0 AF XY: 0.0000378 AC XY: 5AN XY: 132224
GnomAD4 exome AF: 0.0000605 AC: 88AN: 1453522Hom.: 0 Cov.: 33 AF XY: 0.0000705 AC XY: 51AN XY: 723136
GnomAD4 genome AF: 0.0000725 AC: 11AN: 151716Hom.: 0 Cov.: 32 AF XY: 0.0000675 AC XY: 5AN XY: 74064
ClinVar
Submissions by phenotype
DNAJC13-related disorder Uncertain:1
The DNAJC13 c.197C>T variant is predicted to result in the amino acid substitution p.Thr66Met. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.010% of alleles in individuals of South Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/3-132166217-C-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at