chr8-17311512-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_004686.5(MTMR7):c.1100T>C(p.Met367Thr) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,842 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004686.5 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTMR7 | NM_004686.5 | c.1100T>C | p.Met367Thr | missense_variant, splice_region_variant | 9/14 | ENST00000180173.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTMR7 | ENST00000180173.10 | c.1100T>C | p.Met367Thr | missense_variant, splice_region_variant | 9/14 | 1 | NM_004686.5 | P1 | |
MTMR7 | ENST00000521857.5 | c.1100T>C | p.Met367Thr | missense_variant, splice_region_variant | 9/13 | 5 | |||
MTMR7 | ENST00000519590.5 | n.162T>C | splice_region_variant, non_coding_transcript_exon_variant | 1/4 | 4 | ||||
MTMR7 | ENST00000519763.1 | n.236T>C | splice_region_variant, non_coding_transcript_exon_variant | 2/5 | 4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251140Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135694
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461842Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727222
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2023 | The c.1100T>C (p.M367T) alteration is located in exon 9 (coding exon 9) of the MTMR7 gene. This alteration results from a T to C substitution at nucleotide position 1100, causing the methionine (M) at amino acid position 367 to be replaced by a threonine (T). 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