rs750545005
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3
The NM_001270974.2(HYDIN):c.13924C>T(p.Arg4642Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000486 in 152,276 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00049 ( 0 hom., cov: 30)
Exomes 𝑓: 0.00068 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
HYDIN
NM_001270974.2 missense
NM_001270974.2 missense
Scores
7
6
4
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.16
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.826
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HYDIN | ENST00000393567.7 | c.13924C>T | p.Arg4642Cys | missense_variant | Exon 81 of 86 | 5 | NM_001270974.2 | ENSP00000377197.2 | ||
HYDIN | ENST00000378856.8 | n.*2680C>T | non_coding_transcript_exon_variant | Exon 16 of 22 | 1 | ENSP00000463350.1 | ||||
HYDIN | ENST00000378856.8 | n.*2680C>T | 3_prime_UTR_variant | Exon 16 of 22 | 1 | ENSP00000463350.1 |
Frequencies
GnomAD3 genomes AF: 0.000486 AC: 74AN: 152158Hom.: 0 Cov.: 30
GnomAD3 genomes
AF:
AC:
74
AN:
152158
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000148 AC: 1AN: 67476Hom.: 0 AF XY: 0.0000299 AC XY: 1AN XY: 33484
GnomAD3 exomes
AF:
AC:
1
AN:
67476
Hom.:
AF XY:
AC XY:
1
AN XY:
33484
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000681 AC: 995AN: 1460770Hom.: 0 Cov.: 34 AF XY: 0.000687 AC XY: 499AN XY: 726700
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
995
AN:
1460770
Hom.:
Cov.:
34
AF XY:
AC XY:
499
AN XY:
726700
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000486 AC: 74AN: 152276Hom.: 0 Cov.: 30 AF XY: 0.000363 AC XY: 27AN XY: 74466
GnomAD4 genome
AF:
AC:
74
AN:
152276
Hom.:
Cov.:
30
AF XY:
AC XY:
27
AN XY:
74466
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Pathogenic
D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Pathogenic
D
Vest4
MutPred
Loss of MoRF binding (P = 0.0347);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at