chr17-76074893-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003857.4(GALR2):āc.10T>Cā(p.Ser4Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000109 in 1,375,392 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (ā ).
Frequency
Consequence
NM_003857.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALR2 | NM_003857.4 | c.10T>C | p.Ser4Pro | missense_variant | Exon 1 of 2 | ENST00000329003.4 | NP_003848.1 | |
GALR2 | XM_011525427.4 | c.76-237T>C | intron_variant | Intron 2 of 3 | XP_011523729.1 | |||
GALR2 | XM_047436984.1 | c.76-237T>C | intron_variant | Intron 2 of 3 | XP_047292940.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000993 AC: 13AN: 130872Hom.: 0 AF XY: 0.0000989 AC XY: 7AN XY: 70776
GnomAD4 exome AF: 0.0000109 AC: 15AN: 1375392Hom.: 0 Cov.: 32 AF XY: 0.0000148 AC XY: 10AN XY: 677886
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.10T>C (p.S4P) alteration is located in exon 1 (coding exon 1) of the GALR2 gene. This alteration results from a T to C substitution at nucleotide position 10, causing the serine (S) at amino acid position 4 to be replaced by a proline (P). 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