chr16-70818377-G-A
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001270974.2(HYDIN):c.14623C>T(p.Leu4875Leu) variant causes a synonymous 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 27)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
HYDIN
NM_001270974.2 synonymous
NM_001270974.2 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.40
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 Likely_benign. Variant got -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP7
Synonymous conserved (PhyloP=1.4 with no splicing effect.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HYDIN | ENST00000393567.7 | c.14623C>T | p.Leu4875Leu | synonymous_variant | Exon 84 of 86 | 5 | NM_001270974.2 | ENSP00000377197.2 | ||
HYDIN | ENST00000378856.8 | n.*3379C>T | non_coding_transcript_exon_variant | Exon 19 of 22 | 1 | ENSP00000463350.1 | ||||
HYDIN | ENST00000378856.8 | n.*3379C>T | 3_prime_UTR_variant | Exon 19 of 22 | 1 | ENSP00000463350.1 | ||||
HYDIN | ENST00000542283.1 | n.117C>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 5 |
Frequencies
GnomAD3 genomes Cov.: 27
GnomAD3 genomes
Cov.:
27
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1461410Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727008
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
1461410
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
727008
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 27
GnomAD4 genome
Cov.:
27
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at