X-150731569-G-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001306144.3(MTMR1):c.841G>T(p.Asp281Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000357 in 1,205,896 control chromosomes in the GnomAD database, including 1 homozygotes. There are 20 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001306144.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000446 AC: 5AN: 112047Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34189
GnomAD3 exomes AF: 0.0000611 AC: 11AN: 180080Hom.: 0 AF XY: 0.0000928 AC XY: 6AN XY: 64662
GnomAD4 exome AF: 0.0000347 AC: 38AN: 1093849Hom.: 1 Cov.: 29 AF XY: 0.0000556 AC XY: 20AN XY: 359605
GnomAD4 genome AF: 0.0000446 AC: 5AN: 112047Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34189
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.817G>T (p.D273Y) alteration is located in exon 8 (coding exon 8) of the MTMR1 gene. This alteration results from a G to T substitution at nucleotide position 817, causing the aspartic acid (D) at amino acid position 273 to be replaced by a tyrosine (Y). 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