5-3596197-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_024337.4(IRX1):c.92C>T(p.Ala31Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000184 in 1,037,504 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024337.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IRX1 | NM_024337.4 | c.92C>T | p.Ala31Val | missense_variant | 1/4 | ENST00000302006.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IRX1 | ENST00000302006.4 | c.92C>T | p.Ala31Val | missense_variant | 1/4 | 1 | NM_024337.4 | P1 | |
ENST00000559410.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.000259 AC: 38AN: 146976Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0120 AC: 3AN: 250Hom.: 0 AF XY: 0.00714 AC XY: 1AN XY: 140
GnomAD4 exome AF: 0.000172 AC: 153AN: 890432Hom.: 1 Cov.: 30 AF XY: 0.000178 AC XY: 74AN XY: 415352
GnomAD4 genome AF: 0.000258 AC: 38AN: 147072Hom.: 0 Cov.: 33 AF XY: 0.000307 AC XY: 22AN XY: 71612
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.92C>T (p.A31V) alteration is located in exon 1 (coding exon 1) of the IRX1 gene. This alteration results from a C to T substitution at nucleotide position 92, causing the alanine (A) at amino acid position 31 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at