rs12449210
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001270974.2(HYDIN):c.-82A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.339 in 1,535,590 control chromosomes in the GnomAD database, including 91,219 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001270974.2 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HYDIN | NM_001270974.2 | c.-82A>T | 5_prime_UTR_variant | Exon 1 of 86 | ENST00000393567.7 | NP_001257903.1 | ||
HYDIN | NM_017558.5 | c.-82A>T | 5_prime_UTR_variant | Exon 1 of 20 | NP_060028.2 | |||
HYDIN | NM_001198542.1 | c.58+10A>T | intron_variant | Intron 1 of 18 | NP_001185471.1 | |||
HYDIN | NM_001198543.1 | c.28+40A>T | intron_variant | Intron 1 of 18 | NP_001185472.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.348 AC: 52884AN: 151774Hom.: 9673 Cov.: 32
GnomAD3 exomes AF: 0.400 AC: 54708AN: 136730Hom.: 11809 AF XY: 0.391 AC XY: 29013AN XY: 74238
GnomAD4 exome AF: 0.337 AC: 466950AN: 1383696Hom.: 81516 Cov.: 38 AF XY: 0.338 AC XY: 230883AN XY: 682790
GnomAD4 genome AF: 0.349 AC: 52968AN: 151894Hom.: 9703 Cov.: 32 AF XY: 0.349 AC XY: 25872AN XY: 74236
ClinVar
Submissions by phenotype
not specified Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -
not provided Benign:1
- -
Primary ciliary dyskinesia 5 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at