rs750545005

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

Scores

7
6
4

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.16
Variant links:
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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HYDINNM_001270974.2 linkc.13924C>T p.Arg4642Cys missense_variant Exon 81 of 86 ENST00000393567.7 NP_001257903.1 Q4G0P3-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
HYDINENST00000393567.7 linkc.13924C>T p.Arg4642Cys missense_variant Exon 81 of 86 5 NM_001270974.2 ENSP00000377197.2 Q4G0P3-1
HYDINENST00000378856.8 linkn.*2680C>T non_coding_transcript_exon_variant Exon 16 of 22 1 ENSP00000463350.1 J3QL30
HYDINENST00000378856.8 linkn.*2680C>T 3_prime_UTR_variant Exon 16 of 22 1 ENSP00000463350.1 J3QL30

Frequencies

GnomAD3 genomes
AF:
0.000486
AC:
74
AN:
152158
Hom.:
0
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.000169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000458
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000780
Gnomad OTH
AF:
0.00239
GnomAD3 exomes
AF:
0.0000148
AC:
1
AN:
67476
Hom.:
0
AF XY:
0.0000299
AC XY:
1
AN XY:
33484
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000123
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.000681
AC:
995
AN:
1460770
Hom.:
0
Cov.:
34
AF XY:
0.000687
AC XY:
499
AN XY:
726700
show subpopulations
Gnomad4 AFR exome
AF:
0.000209
Gnomad4 AMR exome
AF:
0.000895
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000650
Gnomad4 FIN exome
AF:
0.0000374
Gnomad4 NFE exome
AF:
0.000759
Gnomad4 OTH exome
AF:
0.000746
GnomAD4 genome
AF:
0.000486
AC:
74
AN:
152276
Hom.:
0
Cov.:
30
AF XY:
0.000363
AC XY:
27
AN XY:
74466
show subpopulations
Gnomad4 AFR
AF:
0.000168
Gnomad4 AMR
AF:
0.000458
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000780
Gnomad4 OTH
AF:
0.00237

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.85
BayesDel_addAF
Pathogenic
0.23
D
BayesDel_noAF
Uncertain
0.090
CADD
Pathogenic
27
DANN
Uncertain
1.0
DEOGEN2
Benign
0.40
T
Eigen
Pathogenic
0.74
Eigen_PC
Uncertain
0.66
FATHMM_MKL
Uncertain
0.97
D
M_CAP
Benign
0.036
D
MetaRNN
Pathogenic
0.83
D
MetaSVM
Benign
-1.2
T
MutationAssessor
Pathogenic
3.2
M
PrimateAI
Uncertain
0.73
T
PROVEAN
Pathogenic
-7.8
D
REVEL
Uncertain
0.38
Sift
Pathogenic
0.0
D
Vest4
0.85
MutPred
0.64
Loss of MoRF binding (P = 0.0347);
MVP
0.29
ClinPred
0.99
D
GERP RS
5.0
Varity_R
0.63
gMVP
0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs750545005; hg19: chr16-70863709; COSMIC: COSV101124817; API