2-232456434-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_001631.5(ALPI):c.153C>T(p.Val51Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,614,026 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_001631.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALPI | NM_001631.5 | c.153C>T | p.Val51Val | synonymous_variant | Exon 2 of 11 | ENST00000295463.4 | NP_001622.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALPI | ENST00000295463.4 | c.153C>T | p.Val51Val | synonymous_variant | Exon 2 of 11 | 1 | NM_001631.5 | ENSP00000295463.3 | ||
ALPI | ENST00000457560.1 | n.*82C>T | non_coding_transcript_exon_variant | Exon 1 of 10 | 5 | ENSP00000413068.1 | ||||
ALPI | ENST00000457560.1 | n.*82C>T | 3_prime_UTR_variant | Exon 1 of 10 | 5 | ENSP00000413068.1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251348Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135868
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461794Hom.: 0 Cov.: 33 AF XY: 0.0000316 AC XY: 23AN XY: 727214
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74436
ClinVar
Submissions by phenotype
ALPI-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