19-10833137-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_006858.4(TMED1):c.542G>A(p.Arg181His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,461,682 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006858.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMED1 | NM_006858.4 | c.542G>A | p.Arg181His | missense_variant | Exon 4 of 4 | ENST00000214869.7 | NP_006849.1 | |
TMED1 | XM_006722631.4 | c.428G>A | p.Arg143His | missense_variant | Exon 4 of 4 | XP_006722694.1 | ||
TMED1 | NR_104015.2 | n.497G>A | non_coding_transcript_exon_variant | Exon 4 of 4 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251230Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135866
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461682Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727168
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.542G>A (p.R181H) alteration is located in exon 4 (coding exon 4) of the TMED1 gene. This alteration results from a G to A substitution at nucleotide position 542, causing the arginine (R) at amino acid position 181 to be replaced by a histidine (H). 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