16-70921012-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001270974.2(HYDIN):​c.7364C>G​(p.Pro2455Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P2455Q) has been classified as Benign.

Frequency

Genomes: not found (cov: 24)
Exomes š‘“: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

HYDIN
NM_001270974.2 missense

Scores

17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.45
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]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.09032071).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
HYDINNM_001270974.2 linkc.7364C>G p.Pro2455Arg missense_variant Exon 46 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.7364C>G p.Pro2455Arg missense_variant Exon 46 of 86 5 NM_001270974.2 ENSP00000377197.2 Q4G0P3-1
HYDINENST00000309900.11 linkn.2036C>G non_coding_transcript_exon_variant Exon 12 of 20 1

Frequencies

GnomAD3 genomes
Cov.:
24
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
1425638
Hom.:
0
Cov.:
25
AF XY:
0.00
AC XY:
0
AN XY:
709018
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
24

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.067
BayesDel_addAF
Benign
-0.30
T
BayesDel_noAF
Benign
-0.67
CADD
Benign
16
DANN
Benign
0.62
DEOGEN2
Benign
0.019
T
Eigen
Benign
-0.67
Eigen_PC
Benign
-0.46
FATHMM_MKL
Benign
0.60
D
M_CAP
Benign
0.020
T
MetaRNN
Benign
0.090
T
MetaSVM
Benign
-0.81
T
MutationAssessor
Benign
0.0
N
PrimateAI
Benign
0.35
T
PROVEAN
Benign
0.76
N
REVEL
Benign
0.17
Sift
Benign
0.41
T
Vest4
0.11
MutPred
0.23
Gain of MoRF binding (P = 0.0084);
MVP
0.30
ClinPred
0.41
T
GERP RS
5.9
Varity_R
0.034
gMVP
0.060

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: rs1798531; hg19: chr16-70954915; API