chr8-17299947-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_004686.5(MTMR7):c.1898G>C(p.Arg633Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000186 in 1,613,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 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. R633W) 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 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTMR7 | NM_004686.5 | c.1898G>C | p.Arg633Pro | missense_variant | 14/14 | ENST00000180173.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTMR7 | ENST00000180173.10 | c.1898G>C | p.Arg633Pro | missense_variant | 14/14 | 1 | NM_004686.5 | P1 | |
VPS37A | ENST00000520997.1 | n.292C>G | non_coding_transcript_exon_variant | 3/3 | 3 | ||||
VPS37A | ENST00000521162.5 | n.634C>G | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
VPS37A | ENST00000519515.1 | n.52+1789C>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251216Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135764
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461842Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727222
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74306
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 06, 2022 | The c.1898G>C (p.R633P) alteration is located in exon 14 (coding exon 14) of the MTMR7 gene. This alteration results from a G to C substitution at nucleotide position 1898, causing the arginine (R) at amino acid position 633 to be replaced by a proline (P). 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