7-7234398-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020156.5(C1GALT1):āc.79T>Cā(p.Phe27Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,860 control chromosomes in the GnomAD database, including 1 homozygotes. 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 (ā ).
Frequency
Consequence
NM_020156.5 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C1GALT1 | NM_020156.5 | c.79T>C | p.Phe27Leu | missense_variant | 2/4 | ENST00000436587.7 | NP_064541.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152200Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251276Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135824
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461660Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727112
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152200Hom.: 1 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2024 | The c.79T>C (p.F27L) alteration is located in exon 2 (coding exon 1) of the C1GALT1 gene. This alteration results from a T to C substitution at nucleotide position 79, causing the phenylalanine (F) at amino acid position 27 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