chr5-1880777-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_016358.3(IRX4):c.355G>A(p.Ala119Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 1,613,276 control chromosomes in the GnomAD database, including 30,377 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_016358.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRX4 | NM_016358.3 | c.355G>A | p.Ala119Thr | missense_variant | 3/5 | ENST00000231357.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRX4 | ENST00000231357.7 | c.355G>A | p.Ala119Thr | missense_variant | 3/5 | 1 | NM_016358.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.194 AC: 29502AN: 151854Hom.: 3001 Cov.: 31
GnomAD3 exomes AF: 0.167 AC: 41884AN: 251104Hom.: 4141 AF XY: 0.166 AC XY: 22597AN XY: 135812
GnomAD4 exome AF: 0.188 AC: 274538AN: 1461306Hom.: 27362 Cov.: 33 AF XY: 0.185 AC XY: 134771AN XY: 726986
GnomAD4 genome ? AF: 0.194 AC: 29541AN: 151970Hom.: 3015 Cov.: 31 AF XY: 0.191 AC XY: 14221AN XY: 74300
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 10, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at