chr1-11788023-G-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001010881.2(C1orf167):c.3824G>A(p.Ser1275Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00133 in 1,301,232 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001010881.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
C1orf167 | NM_001010881.2 | c.3824G>A | p.Ser1275Asn | missense_variant | Exon 18 of 21 | ENST00000688073.1 | NP_001010881.1 | |
MTHFR | NM_005957.5 | c.*2657C>T | 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>A | p.Ser1275Asn | missense_variant | Exon 18 of 21 | NM_001010881.2 | ENSP00000510540.1 | |||
MTHFR | ENST00000376590 | c.*2657C>T | 3_prime_UTR_variant | Exon 12 of 12 | 1 | NM_005957.5 | ENSP00000365775.3 |
Frequencies
GnomAD3 genomes AF: 0.00120 AC: 182AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00125 AC: 185AN: 147914Hom.: 1 AF XY: 0.00119 AC XY: 95AN XY: 79538
GnomAD4 exome AF: 0.00135 AC: 1551AN: 1148882Hom.: 3 Cov.: 31 AF XY: 0.00135 AC XY: 763AN XY: 563252
GnomAD4 genome AF: 0.00119 AC: 182AN: 152350Hom.: 0 Cov.: 33 AF XY: 0.00102 AC XY: 76AN XY: 74502
ClinVar
Submissions by phenotype
Homocystinuria due to methylene tetrahydrofolate reductase deficiency Uncertain:1
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
not provided Benign:1
C1orf167: BP4 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at