rs1553959113
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_172250.3(MMAA):c.970-2A>T variant causes a splice acceptor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,710 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_172250.3 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MMAA | NM_172250.3 | c.970-2A>T | splice_acceptor_variant | ENST00000649156.2 | NP_758454.1 | |||
MMAA | NM_001375644.1 | c.970-2A>T | splice_acceptor_variant | NP_001362573.1 | ||||
MMAA | XM_011531684.4 | c.970-2A>T | splice_acceptor_variant | XP_011529986.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MMAA | ENST00000649156.2 | c.970-2A>T | splice_acceptor_variant | NM_172250.3 | ENSP00000497008 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461710Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727156
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Methylmalonic aciduria, cblA type Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Dec 08, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at