chr8-96243980-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015942.5(MTERF3):c.998C>T(p.Thr333Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000108 in 1,613,948 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_015942.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MTERF3 | NM_015942.5 | c.998C>T | p.Thr333Met | missense_variant | 7/8 | ENST00000287025.4 | |
MTERF3 | NM_001286643.1 | c.998C>T | p.Thr333Met | missense_variant | 7/9 | ||
MTERF3 | NM_001362964.1 | c.428C>T | p.Thr143Met | missense_variant | 7/8 | ||
MTERF3 | XM_011517054.3 | c.659C>T | p.Thr220Met | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTERF3 | ENST00000287025.4 | c.998C>T | p.Thr333Met | missense_variant | 7/8 | 1 | NM_015942.5 | P1 | |
MTERF3 | ENST00000523821.5 | c.998C>T | p.Thr333Met | missense_variant | 7/9 | 1 | |||
MTERF3 | ENST00000522822.5 | c.635C>T | p.Thr212Met | missense_variant | 5/6 | 2 | |||
MTERF3 | ENST00000524341.5 | c.327+1880C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251476Hom.: 0 AF XY: 0.0000956 AC XY: 13AN XY: 135916
GnomAD4 exome AF: 0.000105 AC: 153AN: 1461794Hom.: 0 Cov.: 31 AF XY: 0.000102 AC XY: 74AN XY: 727214
GnomAD4 genome ? AF: 0.000145 AC: 22AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2022 | The c.998C>T (p.T333M) alteration is located in exon 7 (coding exon 6) of the MTERF3 gene. This alteration results from a C to T substitution at nucleotide position 998, causing the threonine (T) at amino acid position 333 to be replaced by a methionine (M). 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