NM_015942.5:c.643A>G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015942.5(MTERF3):c.643A>G(p.Ile215Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000684 in 1,609,238 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTERF3 | NM_015942.5 | c.643A>G | p.Ile215Val | missense_variant | Exon 4 of 8 | ENST00000287025.4 | NP_057026.3 | |
MTERF3 | NM_001286643.1 | c.643A>G | p.Ile215Val | missense_variant | Exon 4 of 9 | NP_001273572.1 | ||
MTERF3 | NM_001362964.1 | c.73A>G | p.Ile25Val | missense_variant | Exon 4 of 8 | NP_001349893.1 | ||
MTERF3 | XM_011517054.3 | c.304A>G | p.Ile102Val | missense_variant | Exon 4 of 8 | XP_011515356.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTERF3 | ENST00000287025.4 | c.643A>G | p.Ile215Val | missense_variant | Exon 4 of 8 | 1 | NM_015942.5 | ENSP00000287025.3 | ||
MTERF3 | ENST00000523821.5 | c.643A>G | p.Ile215Val | missense_variant | Exon 4 of 9 | 1 | ENSP00000429400.1 | |||
MTERF3 | ENST00000522822.5 | c.280A>G | p.Ile94Val | missense_variant | Exon 2 of 6 | 2 | ENSP00000430138.1 | |||
MTERF3 | ENST00000524341.5 | c.73A>G | p.Ile25Val | missense_variant | Exon 2 of 5 | 3 | ENSP00000429267.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 151990Hom.: 0 Cov.: 30
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 246528Hom.: 0 AF XY: 0.0000300 AC XY: 4AN XY: 133256
GnomAD4 exome AF: 0.00000549 AC: 8AN: 1457248Hom.: 0 Cov.: 31 AF XY: 0.00000828 AC XY: 6AN XY: 724800
GnomAD4 genome AF: 0.0000197 AC: 3AN: 151990Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74266
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.643A>G (p.I215V) alteration is located in exon 4 (coding exon 3) of the MTERF3 gene. This alteration results from a A to G substitution at nucleotide position 643, causing the isoleucine (I) at amino acid position 215 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