8-17299948-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004686.5(MTMR7):c.1897C>T(p.Arg633Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R633P) has been classified as Uncertain significance.
Frequency
Consequence
NM_004686.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTMR7 | NM_004686.5 | c.1897C>T | p.Arg633Trp | missense_variant | 14/14 | ENST00000180173.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTMR7 | ENST00000180173.10 | c.1897C>T | p.Arg633Trp | missense_variant | 14/14 | 1 | NM_004686.5 | P1 | |
VPS37A | ENST00000520997.1 | n.293G>A | non_coding_transcript_exon_variant | 3/3 | 3 | ||||
VPS37A | ENST00000521162.5 | n.635G>A | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
VPS37A | ENST00000519515.1 | n.52+1790G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251212Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135760
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461838Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727218
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152132Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74308
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2023 | The c.1897C>T (p.R633W) alteration is located in exon 14 (coding exon 14) of the MTMR7 gene. This alteration results from a C to T substitution at nucleotide position 1897, causing the arginine (R) at amino acid position 633 to be replaced by a tryptophan (W). 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