1-37815464-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_005955.3(MTF1):c.1934G>A(p.Arg645Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000125 in 1,603,928 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R645W) has been classified as Uncertain significance.
Frequency
Consequence
NM_005955.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTF1 | NM_005955.3 | c.1934G>A | p.Arg645Gln | missense_variant | Exon 11 of 11 | ENST00000373036.5 | NP_005946.2 | |
MTF1 | XM_011541491.3 | c.1934G>A | p.Arg645Gln | missense_variant | Exon 11 of 11 | XP_011539793.1 | ||
MTF1 | XM_047421170.1 | c.1934G>A | p.Arg645Gln | missense_variant | Exon 12 of 12 | XP_047277126.1 | ||
MTF1 | XM_047421173.1 | c.1007G>A | p.Arg336Gln | missense_variant | Exon 10 of 10 | XP_047277129.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000415 AC: 1AN: 241082Hom.: 0 AF XY: 0.00000767 AC XY: 1AN XY: 130332
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1451840Hom.: 0 Cov.: 31 AF XY: 0.00000831 AC XY: 6AN XY: 721634
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1934G>A (p.R645Q) alteration is located in exon 11 (coding exon 10) of the MTF1 gene. This alteration results from a G to A substitution at nucleotide position 1934, causing the arginine (R) at amino acid position 645 to be replaced by a glutamine (Q). 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