rs577029897
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001190787.3(MCIDAS):c.93C>T(p.Leu31=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000197 in 1,519,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L31L) has been classified as Likely benign.
Frequency
Consequence
NM_001190787.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MCIDAS | NM_001190787.3 | c.93C>T | p.Leu31= | synonymous_variant | 1/7 | ENST00000513312.3 | |
LOC124900978 | XR_007058773.1 | n.429G>A | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MCIDAS | ENST00000513312.3 | c.93C>T | p.Leu31= | synonymous_variant | 1/7 | 1 | NM_001190787.3 | P1 | |
MCIDAS | ENST00000513468.5 | c.93C>T | p.Leu31= | synonymous_variant, NMD_transcript_variant | 1/7 | 5 | |||
MCIDAS | ENST00000515336.1 | n.58-115C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000146 AC: 2AN: 1367552Hom.: 0 Cov.: 31 AF XY: 0.00000148 AC XY: 1AN XY: 674924
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74372
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at