chr17-11598540-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM2BP4_StrongBP6BS1
The NM_001372.4(DNAH9):āc.42C>Gā(p.Asn14Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000327 in 1,402,268 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001372.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAH9 | NM_001372.4 | c.42C>G | p.Asn14Lys | missense_variant | 1/69 | ENST00000262442.9 | NP_001363.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAH9 | ENST00000262442.9 | c.42C>G | p.Asn14Lys | missense_variant | 1/69 | 1 | NM_001372.4 | ENSP00000262442 | P1 | |
DNAH9 | ENST00000579406.1 | n.69C>G | non_coding_transcript_exon_variant | 1/8 | 1 | |||||
DNAH9 | ENST00000454412.6 | c.42C>G | p.Asn14Lys | missense_variant | 1/68 | 5 | ENSP00000414874 | |||
DNAH9 | ENST00000579828.5 | c.42C>G | p.Asn14Lys | missense_variant | 1/4 | 2 | ENSP00000463782 |
Frequencies
GnomAD3 genomes AF: 0.00177 AC: 259AN: 146632Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000292 AC: 9AN: 30774Hom.: 0 AF XY: 0.000279 AC XY: 5AN XY: 17928
GnomAD4 exome AF: 0.000159 AC: 199AN: 1255522Hom.: 0 Cov.: 33 AF XY: 0.000155 AC XY: 95AN XY: 613442
GnomAD4 genome AF: 0.00177 AC: 260AN: 146746Hom.: 0 Cov.: 31 AF XY: 0.00162 AC XY: 116AN XY: 71574
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 20, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2023 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2023 | The c.42C>G (p.N14K) alteration is located in exon 1 (coding exon 1) of the DNAH9 gene. This alteration results from a C to G substitution at nucleotide position 42, causing the asparagine (N) at amino acid position 14 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
DNAH9-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 31, 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