4-74158250-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001144978.3(MTHFD2L):c.112G>C(p.Ala38Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000171 in 1,462,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001144978.3 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 | UniProt |
---|---|---|---|---|---|---|---|
MTHFD2L | NM_001144978.3 | c.112G>C | p.Ala38Pro | missense_variant | 1/8 | ENST00000325278.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTHFD2L | ENST00000325278.7 | c.112G>C | p.Ala38Pro | missense_variant | 1/8 | 5 | NM_001144978.3 | P1 | |
ENST00000600169.2 | n.124C>G | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152038Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000303 AC: 2AN: 65974Hom.: 0 AF XY: 0.0000577 AC XY: 2AN XY: 34652
GnomAD4 exome AF: 0.0000130 AC: 17AN: 1310650Hom.: 0 Cov.: 31 AF XY: 0.0000141 AC XY: 9AN XY: 639170
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 25, 2023 | The c.112G>C (p.A38P) alteration is located in exon 1 (coding exon 1) of the MTHFD2L gene. This alteration results from a G to C substitution at nucleotide position 112, causing the alanine (A) at amino acid position 38 to be replaced by a proline (P). 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