2-232456669-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBS1_SupportingBS2
The NM_001631.5(ALPI):c.274C>T(p.Arg92Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00107 in 1,609,262 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001631.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ALPI | NM_001631.5 | c.274C>T | p.Arg92Cys | missense_variant | Exon 3 of 11 | ENST00000295463.4 | NP_001622.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ALPI | ENST00000295463.4 | c.274C>T | p.Arg92Cys | missense_variant | Exon 3 of 11 | 1 | NM_001631.5 | ENSP00000295463.3 | ||
ALPI | ENST00000457560.1 | n.*203C>T | non_coding_transcript_exon_variant | Exon 2 of 10 | 5 | ENSP00000413068.1 | ||||
ALPI | ENST00000457560.1 | n.*203C>T | 3_prime_UTR_variant | Exon 2 of 10 | 5 | ENSP00000413068.1 |
Frequencies
GnomAD3 genomes AF: 0.00553 AC: 841AN: 151970Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.00141 AC: 338AN: 240484Hom.: 0 AF XY: 0.00110 AC XY: 143AN XY: 130156
GnomAD4 exome AF: 0.000608 AC: 886AN: 1457174Hom.: 6 Cov.: 33 AF XY: 0.000534 AC XY: 387AN XY: 724526
GnomAD4 genome AF: 0.00554 AC: 842AN: 152088Hom.: 6 Cov.: 32 AF XY: 0.00499 AC XY: 371AN XY: 74340
ClinVar
Submissions by phenotype
not provided Uncertain:1
BS1 -
ALPI-related disorder Benign:1
This variant is classified as 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