chrX-120626501-C-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001011551.3(C1GALT1C1):c.666G>C(p.Gln222His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000315 in 1,210,871 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 175 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_001011551.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C1GALT1C1 | NM_001011551.3 | c.666G>C | p.Gln222His | missense_variant | 2/2 | ENST00000304661.6 | |
C1GALT1C1 | NM_152692.5 | c.666G>C | p.Gln222His | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C1GALT1C1 | ENST00000304661.6 | c.666G>C | p.Gln222His | missense_variant | 2/2 | 1 | NM_001011551.3 | P1 | |
C1GALT1C1 | ENST00000371313.2 | c.666G>C | p.Gln222His | missense_variant | 3/3 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000222 AC: 25AN: 112692Hom.: 0 Cov.: 24 AF XY: 0.000230 AC XY: 8AN XY: 34834
GnomAD3 exomes AF: 0.000393 AC: 72AN: 183344Hom.: 0 AF XY: 0.000560 AC XY: 38AN XY: 67820
GnomAD4 exome AF: 0.000325 AC: 357AN: 1098124Hom.: 0 Cov.: 31 AF XY: 0.000459 AC XY: 167AN XY: 363498
GnomAD4 genome ? AF: 0.000222 AC: 25AN: 112747Hom.: 0 Cov.: 24 AF XY: 0.000229 AC XY: 8AN XY: 34899
ClinVar
Submissions by phenotype
Polyagglutinable erythrocyte syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 14, 2023 | - - |
C1GALT1C1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 23, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at