rs755218771
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The ENST00000374080.8(MED12):c.4806G>A(p.Ser1602=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,209,106 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. S1602S) has been classified as Likely benign.
Frequency
Consequence
ENST00000374080.8 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MED12 | NM_005120.3 | c.4806G>A | p.Ser1602= | synonymous_variant | 35/45 | ENST00000374080.8 | NP_005111.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MED12 | ENST00000374080.8 | c.4806G>A | p.Ser1602= | synonymous_variant | 35/45 | 1 | NM_005120.3 | ENSP00000363193 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000901 AC: 1AN: 110971Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33185
GnomAD3 exomes AF: 0.00000550 AC: 1AN: 181863Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67685
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1098135Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 1AN XY: 363495
GnomAD4 genome AF: 0.00000901 AC: 1AN: 110971Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33185
ClinVar
Submissions by phenotype
FG syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 10, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at