chr8-96258572-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015942.5(MTERF3):c.119G>T(p.Gly40Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000057 in 1,614,090 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.119G>T | p.Gly40Val | missense_variant | 2/8 | ENST00000287025.4 | |
MTERF3 | NM_001286643.1 | c.119G>T | p.Gly40Val | missense_variant | 2/9 | ||
MTERF3 | NM_001362964.1 | c.-417G>T | 5_prime_UTR_variant | 2/8 | |||
MTERF3 | XM_011517054.3 | c.-351G>T | 5_prime_UTR_variant | 2/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTERF3 | ENST00000287025.4 | c.119G>T | p.Gly40Val | missense_variant | 2/8 | 1 | NM_015942.5 | P1 | |
MTERF3 | ENST00000523821.5 | c.119G>T | p.Gly40Val | missense_variant | 2/9 | 1 | |||
MTERF3 | ENST00000517720.1 | c.119G>T | p.Gly40Val | missense_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152152Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251450Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135896
GnomAD4 exome AF: 0.0000616 AC: 90AN: 1461818Hom.: 0 Cov.: 31 AF XY: 0.0000605 AC XY: 44AN XY: 727208
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152272Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2022 | The c.119G>T (p.G40V) alteration is located in exon 2 (coding exon 1) of the MTERF3 gene. This alteration results from a G to T substitution at nucleotide position 119, causing the glycine (G) at amino acid position 40 to be replaced by a valine (V). 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