chr19-56183207-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_033106.4(GALP):c.290T>C(p.Ile97Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000154 in 1,612,678 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_033106.4 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 |
---|---|---|---|---|---|---|---|
GALP | NM_033106.4 | c.290T>C | p.Ile97Thr | missense_variant | 5/6 | ENST00000357330.7 | |
GALP | NM_001145546.2 | c.*91T>C | 3_prime_UTR_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GALP | ENST00000357330.7 | c.290T>C | p.Ile97Thr | missense_variant | 5/6 | 1 | NM_033106.4 | P2 | |
GALP | ENST00000440823.1 | c.*91T>C | 3_prime_UTR_variant | 4/5 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000923 AC: 14AN: 151756Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251478Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135914
GnomAD4 exome AF: 0.000161 AC: 235AN: 1460804Hom.: 0 Cov.: 30 AF XY: 0.000173 AC XY: 126AN XY: 726798
GnomAD4 genome ? AF: 0.0000922 AC: 14AN: 151874Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74190
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.290T>C (p.I97T) alteration is located in exon 5 (coding exon 4) of the GALP gene. This alteration results from a T to C substitution at nucleotide position 290, causing the isoleucine (I) at amino acid position 97 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