chr7-103316015-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014377.3(DNAJC2):c.1501G>A(p.Gly501Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,448,482 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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.1501G>A | p.Gly501Ser | missense_variant | 14/17 | ENST00000379263.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJC2 | ENST00000379263.8 | c.1501G>A | p.Gly501Ser | missense_variant | 14/17 | 1 | NM_014377.3 | P1 | |
ENST00000687345.1 | n.847C>T | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000414 AC: 1AN: 241618Hom.: 0 AF XY: 0.00000762 AC XY: 1AN XY: 131180
GnomAD4 exome AF: 6.90e-7 AC: 1AN: 1448482Hom.: 0 Cov.: 30 AF XY: 0.00000139 AC XY: 1AN XY: 719254
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 22, 2023 | The c.1501G>A (p.G501S) alteration is located in exon 14 (coding exon 14) of the DNAJC2 gene. This alteration results from a G to A substitution at nucleotide position 1501, causing the glycine (G) at amino acid position 501 to be replaced by a serine (S). 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