NM_005955.3:c.1972C>T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005955.3(MTF1):c.1972C>T(p.Pro658Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,612,632 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P658A) has been classified as Uncertain significance.
Frequency
Consequence
NM_005955.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MTF1 | NM_005955.3 | c.1972C>T | p.Pro658Ser | missense_variant | Exon 11 of 11 | ENST00000373036.5 | NP_005946.2 | |
MTF1 | XM_011541491.3 | c.1972C>T | p.Pro658Ser | missense_variant | Exon 11 of 11 | XP_011539793.1 | ||
MTF1 | XM_047421170.1 | c.1972C>T | p.Pro658Ser | missense_variant | Exon 12 of 12 | XP_047277126.1 | ||
MTF1 | XM_047421173.1 | c.1045C>T | p.Pro349Ser | missense_variant | Exon 10 of 10 | XP_047277129.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249176Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134840
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460506Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 726402
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74306
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at