1-19683150-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_181719.7(TMCO4):c.1795G>T(p.Ala599Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_181719.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMCO4 | ENST00000294543.11 | c.1795G>T | p.Ala599Ser | missense_variant | Exon 16 of 16 | 1 | NM_181719.7 | ENSP00000294543.6 | ||
TMCO4 | ENST00000375127.5 | c.1657+138G>T | intron_variant | Intron 15 of 15 | 1 | ENSP00000364269.1 | ||||
TMCO4 | ENST00000489814.5 | n.814G>T | non_coding_transcript_exon_variant | Exon 5 of 5 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1795G>T (p.A599S) alteration is located in exon 16 (coding exon 13) of the TMCO4 gene. This alteration results from a G to T substitution at nucleotide position 1795, causing the alanine (A) at amino acid position 599 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.