NM_005932.4:c.1975G>T
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_ModerateBP6_Moderate
The NM_005932.4(MIPEP):c.1975G>T(p.Ala659Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,612,674 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A659A) has been classified as Likely benign.
Frequency
Consequence
NM_005932.4 missense
Scores
Clinical Significance
Conservation
Publications
- lethal left ventricular non-compaction-seizures-hypotonia-cataract-developmental delay syndromeInheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Broad Center for Mendelian Genomics
- mitochondrial diseaseInheritance: AR Classification: MODERATE Submitted by: ClinGen
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ACMG classification
Our verdict: Likely_benign. The variant received -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MIPEP | ENST00000382172.4 | c.1975G>T | p.Ala659Ser | missense_variant | Exon 18 of 19 | 1 | NM_005932.4 | ENSP00000371607.3 | ||
MIPEP | ENST00000433710.2 | n.168G>T | non_coding_transcript_exon_variant | Exon 3 of 4 | 3 | |||||
MIPEP | ENST00000464194.3 | n.217G>T | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152250Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.00 AC: 0AN: 250278 AF XY: 0.00
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1460424Hom.: 0 Cov.: 30 AF XY: 0.00000826 AC XY: 6AN XY: 726624 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152250Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74388 show subpopulations
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at