11-93784504-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_004268.5(MED17):c.-10C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000251 in 1,592,544 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004268.5 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MED17 | ENST00000251871 | c.-10C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 12 | 1 | NM_004268.5 | ENSP00000251871.3 | |||
MED17 | ENST00000251871 | c.-10C>T | 5_prime_UTR_variant | Exon 1 of 12 | 1 | NM_004268.5 | ENSP00000251871.3 | |||
ENSG00000284057 | ENST00000638767.1 | c.676-124C>T | intron_variant | Intron 7 of 18 | 5 | ENSP00000492220.1 |
Frequencies
GnomAD3 genomes AF: 0.000276 AC: 42AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000365 AC: 88AN: 241058Hom.: 0 AF XY: 0.000304 AC XY: 40AN XY: 131750
GnomAD4 exome AF: 0.000248 AC: 357AN: 1440252Hom.: 1 Cov.: 29 AF XY: 0.000217 AC XY: 155AN XY: 712864
GnomAD4 genome AF: 0.000276 AC: 42AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74468
ClinVar
Submissions by phenotype
Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly Uncertain:1
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MED17-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at