rs1131449
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The ENST00000366577.10(MTR):āc.3576C>Gā(p.Leu1192=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000021 in 1,428,854 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. L1192L) has been classified as Benign.
Frequency
Consequence
ENST00000366577.10 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTR | NM_000254.3 | c.3576C>G | p.Leu1192= | synonymous_variant | 31/33 | ENST00000366577.10 | NP_000245.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTR | ENST00000366577.10 | c.3576C>G | p.Leu1192= | synonymous_variant | 31/33 | 1 | NM_000254.3 | ENSP00000355536 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000507 AC: 1AN: 197208Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 105676
GnomAD4 exome AF: 0.00000210 AC: 3AN: 1428854Hom.: 0 Cov.: 65 AF XY: 0.00 AC XY: 0AN XY: 707630
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Methylcobalamin deficiency type cblG Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at