chr15-40768023-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_018163.3(DNAJC17):c.832A>G(p.Met278Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00254 in 1,598,502 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_018163.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNAJC17 | NM_018163.3 | c.832A>G | p.Met278Val | missense_variant | 11/11 | ENST00000220496.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAJC17 | ENST00000220496.9 | c.832A>G | p.Met278Val | missense_variant | 11/11 | 1 | NM_018163.3 | P1 | |
DNAJC17 | ENST00000558727.1 | n.397A>G | non_coding_transcript_exon_variant | 2/2 | 3 | ||||
DNAJC17 | ENST00000561110.5 | n.379A>G | non_coding_transcript_exon_variant | 5/5 | 3 | ||||
DNAJC17 | ENST00000559238.5 | c.*860A>G | 3_prime_UTR_variant, NMD_transcript_variant | 12/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00189 AC: 288AN: 152174Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.00137 AC: 320AN: 233554Hom.: 1 AF XY: 0.00132 AC XY: 167AN XY: 126832
GnomAD4 exome AF: 0.00260 AC: 3767AN: 1446210Hom.: 9 Cov.: 33 AF XY: 0.00244 AC XY: 1753AN XY: 719516
GnomAD4 genome ? AF: 0.00189 AC: 288AN: 152292Hom.: 2 Cov.: 33 AF XY: 0.00175 AC XY: 130AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at