16-70809809-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_001270974.2(HYDIN):c.14857C>T(p.Arg4953Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00398 in 1,613,950 control chromosomes in the GnomAD database, including 43 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001270974.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HYDIN | ENST00000393567.7 | c.14857C>T | p.Arg4953Trp | missense_variant | Exon 85 of 86 | 5 | NM_001270974.2 | ENSP00000377197.2 | ||
HYDIN | ENST00000378856.8 | n.*3737C>T | non_coding_transcript_exon_variant | Exon 21 of 22 | 1 | ENSP00000463350.1 | ||||
HYDIN | ENST00000378856.8 | n.*3737C>T | 3_prime_UTR_variant | Exon 21 of 22 | 1 | ENSP00000463350.1 |
Frequencies
GnomAD3 genomes AF: 0.00267 AC: 406AN: 152198Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00426 AC: 1063AN: 249564Hom.: 12 AF XY: 0.00498 AC XY: 674AN XY: 135396
GnomAD4 exome AF: 0.00412 AC: 6020AN: 1461634Hom.: 41 Cov.: 31 AF XY: 0.00450 AC XY: 3273AN XY: 727116
GnomAD4 genome AF: 0.00266 AC: 405AN: 152316Hom.: 2 Cov.: 32 AF XY: 0.00278 AC XY: 207AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:2
- -
HYDIN: BP4, BS1, BS2 -
Primary ciliary dyskinesia 5 Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at