19-39391415-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000615911.4(MED29):c.56C>G(p.Ala19Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,611,388 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000615911.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MED29 | NM_017592.4 | c.-8C>G | 5_prime_UTR_variant | Exon 1 of 4 | ENST00000315588.11 | NP_060062.2 | ||
MED29 | NM_001317770.3 | c.-8C>G | 5_prime_UTR_variant | Exon 1 of 4 | NP_001304699.2 | |||
MED29 | NR_133915.3 | n.38C>G | non_coding_transcript_exon_variant | Exon 1 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250182Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135414
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459162Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 725270
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152226Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.56C>G (p.A19G) alteration is located in exon 1 (coding exon 1) of the MED29 gene. This alteration results from a C to G substitution at nucleotide position 56, causing the alanine (A) at amino acid position 19 to be replaced by a glycine (G). 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