NM_001270974.2:c.14886C>T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_001270974.2(HYDIN):c.14886C>T(p.Thr4962Thr) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000319 in 1,598,298 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001270974.2 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HYDIN | ENST00000393567.7 | c.14886C>T | p.Thr4962Thr | splice_region_variant, synonymous_variant | Exon 86 of 86 | 5 | NM_001270974.2 | ENSP00000377197.2 | ||
HYDIN | ENST00000378856.8 | n.*3766C>T | splice_region_variant, non_coding_transcript_exon_variant | Exon 22 of 22 | 1 | ENSP00000463350.1 | ||||
HYDIN | ENST00000378856.8 | n.*3766C>T | 3_prime_UTR_variant | Exon 22 of 22 | 1 | ENSP00000463350.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151980Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 18AN: 238228Hom.: 0 AF XY: 0.0000776 AC XY: 10AN XY: 128864
GnomAD4 exome AF: 0.0000325 AC: 47AN: 1446318Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 29AN XY: 717542
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151980Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74236
ClinVar
Submissions by phenotype
HYDIN-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at