2-9474570-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001039613.3(IAH1):c.4G>A(p.Ala2Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000363 in 1,485,768 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A2V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001039613.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IAH1 | NM_001039613.3 | c.4G>A | p.Ala2Thr | missense_variant | 1/6 | ENST00000497473.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IAH1 | ENST00000497473.6 | c.4G>A | p.Ala2Thr | missense_variant | 1/6 | 1 | NM_001039613.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000266 AC: 4AN: 150550Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000468 AC: 7AN: 149588Hom.: 1 AF XY: 0.0000586 AC XY: 5AN XY: 85330
GnomAD4 exome AF: 0.0000374 AC: 50AN: 1335116Hom.: 1 Cov.: 31 AF XY: 0.0000407 AC XY: 27AN XY: 663662
GnomAD4 genome ? AF: 0.0000266 AC: 4AN: 150652Hom.: 0 Cov.: 33 AF XY: 0.0000136 AC XY: 1AN XY: 73648
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.4G>A (p.A2T) alteration is located in exon 1 (coding exon 1) of the IAH1 gene. This alteration results from a G to A substitution at nucleotide position 4, causing the alanine (A) at amino acid position 2 to be replaced by a threonine (T). 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