chr19-39397506-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_017592.4(MED29):c.410C>T(p.Ser137Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,611,350 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017592.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MED29 | NM_017592.4 | c.410C>T | p.Ser137Phe | missense_variant | Exon 4 of 4 | ENST00000315588.11 | NP_060062.2 | |
MED29 | NM_001317770.3 | c.361-21C>T | intron_variant | Intron 3 of 3 | NP_001304699.2 | |||
MED29 | NR_133915.3 | n.396C>T | non_coding_transcript_exon_variant | Exon 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248896Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134822
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459142Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726042
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.473C>T (p.S158F) alteration is located in exon 4 (coding exon 4) of the MED29 gene. This alteration results from a C to T substitution at nucleotide position 473, causing the serine (S) at amino acid position 158 to be replaced by a phenylalanine (F). 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