1-37815345-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_005955.3(MTF1):c.2053G>A(p.Gly685Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,614,026 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005955.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTF1 | NM_005955.3 | c.2053G>A | p.Gly685Arg | missense_variant | 11/11 | ENST00000373036.5 | NP_005946.2 | |
MTF1 | XM_011541491.3 | c.2053G>A | p.Gly685Arg | missense_variant | 11/11 | XP_011539793.1 | ||
MTF1 | XM_047421170.1 | c.2053G>A | p.Gly685Arg | missense_variant | 12/12 | XP_047277126.1 | ||
MTF1 | XM_047421173.1 | c.1126G>A | p.Gly376Arg | missense_variant | 10/10 | XP_047277129.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MTF1 | ENST00000373036.5 | c.2053G>A | p.Gly685Arg | missense_variant | 11/11 | 1 | NM_005955.3 | ENSP00000362127.3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152020Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250638Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135526
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461888Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727244
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2022 | The c.2053G>A (p.G685R) 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 2053, causing the glycine (G) at amino acid position 685 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