chr17-78424112-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_173628.4(DNAH17):c.13183C>T(p.Arg4395Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000413 in 1,613,604 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R4395Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_173628.4 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 |
---|---|---|---|---|---|---|---|
DNAH17 | NM_173628.4 | c.13183C>T | p.Arg4395Trp | missense_variant | 81/81 | ENST00000389840.7 | |
PGS1 | NM_024419.5 | c.*62G>A | 3_prime_UTR_variant | 10/10 | ENST00000262764.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNAH17 | ENST00000389840.7 | c.13183C>T | p.Arg4395Trp | missense_variant | 81/81 | 5 | NM_173628.4 | P1 | |
PGS1 | ENST00000262764.11 | c.*62G>A | 3_prime_UTR_variant | 10/10 | 1 | NM_024419.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000335 AC: 51AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000766 AC: 191AN: 249452Hom.: 1 AF XY: 0.000845 AC XY: 114AN XY: 134958
GnomAD4 exome AF: 0.000422 AC: 617AN: 1461284Hom.: 3 Cov.: 31 AF XY: 0.000426 AC XY: 310AN XY: 726920
GnomAD4 genome ? AF: 0.000328 AC: 50AN: 152320Hom.: 0 Cov.: 33 AF XY: 0.000430 AC XY: 32AN XY: 74472
ClinVar
Submissions by phenotype
DNAH17-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 27, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at