chr1-25498443-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_018202.6(MACO1):c.1972G>A(p.Val658Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,612,126 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018202.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MACO1 | NM_018202.6 | c.1972G>A | p.Val658Ile | missense_variant | 11/11 | ENST00000374343.5 | |
MACO1 | NM_001282564.2 | c.1291G>A | p.Val431Ile | missense_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MACO1 | ENST00000374343.5 | c.1972G>A | p.Val658Ile | missense_variant | 11/11 | 1 | NM_018202.6 | P1 | |
MACO1 | ENST00000399766.7 | c.1291G>A | p.Val431Ile | missense_variant | 9/9 | 1 | |||
MACO1 | ENST00000647928.1 | c.*800G>A | 3_prime_UTR_variant, NMD_transcript_variant | 11/11 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152056Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248990Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134592
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460070Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726342
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152056Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74254
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.1972G>A (p.V658I) alteration is located in exon 11 (coding exon 11) of the TMEM57 gene. This alteration results from a G to A substitution at nucleotide position 1972, causing the valine (V) at amino acid position 658 to be replaced by an isoleucine (I). 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