chr16-70828385-A-C
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001270974.2(HYDIN):c.14157T>G(p.Tyr4719Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 22)
Exomes 𝑓: 0.0000020 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
HYDIN
NM_001270974.2 stop_gained
NM_001270974.2 stop_gained
Scores
2
5
Clinical Significance
Conservation
PhyloP100: 1.18
Genes affected
HYDIN (HGNC:19368): (HYDIN axonemal central pair apparatus protein) This gene encodes a protein that may be involved in cilia motility. Mutations in this gene cause of autosomal recessive primary ciliary dyskinesia-5, a disorder characterized by the accumulation of cerebrospinal fluid within the ventricles of the brain. A duplicate copy of this gene has been found in humans on chromosome 1. [provided by RefSeq, Jan 2013]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 16-70828385-A-C is Pathogenic according to our data. Variant chr16-70828385-A-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 3027493.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HYDIN | NM_001270974.2 | c.14157T>G | p.Tyr4719Ter | stop_gained | 82/86 | ENST00000393567.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HYDIN | ENST00000393567.7 | c.14157T>G | p.Tyr4719Ter | stop_gained | 82/86 | 5 | NM_001270974.2 | P1 | |
HYDIN | ENST00000378856.8 | c.*2913T>G | 3_prime_UTR_variant, NMD_transcript_variant | 17/22 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD3 genomes
?
Cov.:
22
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000195 AC: 2AN: 1025022Hom.: 0 Cov.: 13 AF XY: 0.00000190 AC XY: 1AN XY: 525364
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
2
AN:
1025022
Hom.:
Cov.:
13
AF XY:
AC XY:
1
AN XY:
525364
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 22
GnomAD4 genome
?
Cov.:
22
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Primary ciliary dyskinesia 5 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Royal Brompton Clinical Genetics And Genomics Laboratory, NHS South East Genomic Laboratory Hub | Mar 06, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
A;A
Vest4
GERP RS
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.