17-76074894-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003857.4(GALR2):c.11C>T(p.Ser4Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000321 in 1,528,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003857.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GALR2 | NM_003857.4 | c.11C>T | p.Ser4Leu | missense_variant | Exon 1 of 2 | ENST00000329003.4 | NP_003848.1 | |
GALR2 | XM_011525427.4 | c.76-236C>T | intron_variant | Intron 2 of 3 | XP_011523729.1 | |||
GALR2 | XM_047436984.1 | c.76-236C>T | intron_variant | Intron 2 of 3 | XP_047292940.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000305 AC: 4AN: 131322Hom.: 0 AF XY: 0.0000141 AC XY: 1AN XY: 71052
GnomAD4 exome AF: 0.00000945 AC: 13AN: 1375754Hom.: 0 Cov.: 32 AF XY: 0.0000103 AC XY: 7AN XY: 678126
GnomAD4 genome AF: 0.000236 AC: 36AN: 152312Hom.: 0 Cov.: 32 AF XY: 0.000255 AC XY: 19AN XY: 74490
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.11C>T (p.S4L) alteration is located in exon 1 (coding exon 1) of the GALR2 gene. This alteration results from a C to T substitution at nucleotide position 11, causing the serine (S) at amino acid position 4 to be replaced by a leucine (L). 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