chr7-103321970-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014377.3(DNAJC2):āc.1045A>Gā(p.Ile349Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000626 in 1,613,846 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 (ā ).
Frequency
Consequence
NM_014377.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJC2 | NM_014377.3 | c.1045A>G | p.Ile349Val | missense_variant | 10/17 | ENST00000379263.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJC2 | ENST00000379263.8 | c.1045A>G | p.Ile349Val | missense_variant | 10/17 | 1 | NM_014377.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000335 AC: 51AN: 152266Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000802 AC: 20AN: 249382Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135300
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461462Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 18AN XY: 727066
GnomAD4 genome AF: 0.000335 AC: 51AN: 152384Hom.: 0 Cov.: 33 AF XY: 0.000322 AC XY: 24AN XY: 74528
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The c.1045A>G (p.I349V) alteration is located in exon 10 (coding exon 10) of the DNAJC2 gene. This alteration results from a A to G substitution at nucleotide position 1045, causing the isoleucine (I) at amino acid position 349 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at