chr8-96258617-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_015942.5(MTERF3):c.74A>G(p.Gln25Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,614,032 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.74A>G | p.Gln25Arg | missense_variant | 2/8 | ENST00000287025.4 | |
MTERF3 | NM_001286643.1 | c.74A>G | p.Gln25Arg | missense_variant | 2/9 | ||
MTERF3 | NM_001362964.1 | c.-462A>G | 5_prime_UTR_variant | 2/8 | |||
MTERF3 | XM_011517054.3 | c.-396A>G | 5_prime_UTR_variant | 2/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MTERF3 | ENST00000287025.4 | c.74A>G | p.Gln25Arg | missense_variant | 2/8 | 1 | NM_015942.5 | P1 | |
MTERF3 | ENST00000523821.5 | c.74A>G | p.Gln25Arg | missense_variant | 2/9 | 1 | |||
MTERF3 | ENST00000517720.1 | c.74A>G | p.Gln25Arg | missense_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251352Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135866
GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461822Hom.: 0 Cov.: 31 AF XY: 0.0000371 AC XY: 27AN XY: 727208
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152210Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2022 | The c.74A>G (p.Q25R) alteration is located in exon 2 (coding exon 1) of the MTERF3 gene. This alteration results from a A to G substitution at nucleotide position 74, causing the glutamine (Q) at amino acid position 25 to be replaced by an arginine (R). 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