rs116730273
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001270974.2(HYDIN):āc.15146T>Gā(p.Met5049Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,316 control chromosomes in the GnomAD database, with no homozygous occurrence. 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.
Frequency
Consequence
NM_001270974.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HYDIN | ENST00000393567.7 | c.15146T>G | p.Met5049Arg | missense_variant | Exon 86 of 86 | 5 | NM_001270974.2 | ENSP00000377197.2 | ||
HYDIN | ENST00000378856.8 | n.*4026T>G | non_coding_transcript_exon_variant | Exon 22 of 22 | 1 | ENSP00000463350.1 | ||||
HYDIN | ENST00000378856.8 | n.*4026T>G | 3_prime_UTR_variant | Exon 22 of 22 | 1 | ENSP00000463350.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249570Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135400
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152316Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74478
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at