1-11788023-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001010881.2(C1orf167):āc.3824G>Cā(p.Ser1275Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000284 in 1,301,114 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S1275N) has been classified as Likely benign.
Frequency
Consequence
NM_001010881.2 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 |
---|---|---|---|---|---|---|---|---|
C1orf167 | NM_001010881.2 | c.3824G>C | p.Ser1275Thr | missense_variant | Exon 18 of 21 | ENST00000688073.1 | NP_001010881.1 | |
MTHFR | NM_005957.5 | c.*2657C>G | 3_prime_UTR_variant | Exon 12 of 12 | ENST00000376590.9 | NP_005948.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
C1orf167 | ENST00000688073.1 | c.3824G>C | p.Ser1275Thr | missense_variant | Exon 18 of 21 | NM_001010881.2 | ENSP00000510540.1 | |||
MTHFR | ENST00000376590 | c.*2657C>G | 3_prime_UTR_variant | Exon 12 of 12 | 1 | NM_005957.5 | ENSP00000365775.3 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000270 AC: 4AN: 147914Hom.: 0 AF XY: 0.0000377 AC XY: 3AN XY: 79538
GnomAD4 exome AF: 0.0000279 AC: 32AN: 1148882Hom.: 0 Cov.: 31 AF XY: 0.0000302 AC XY: 17AN XY: 563252
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74374
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at