chr1-19740902-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_181719.7(TMCO4):c.917G>A(p.Arg306His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000775 in 1,613,778 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMCO4 | NM_181719.7 | c.917G>A | p.Arg306His | missense_variant | 11/16 | ENST00000294543.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMCO4 | ENST00000294543.11 | c.917G>A | p.Arg306His | missense_variant | 11/16 | 1 | NM_181719.7 | P1 | |
TMCO4 | ENST00000375127.5 | c.917G>A | p.Arg306His | missense_variant | 10/16 | 1 | |||
TMCO4 | ENST00000489135.5 | n.803G>A | non_coding_transcript_exon_variant | 7/9 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000132 AC: 33AN: 250154Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135268
GnomAD4 exome AF: 0.0000739 AC: 108AN: 1461444Hom.: 2 Cov.: 31 AF XY: 0.0000812 AC XY: 59AN XY: 727034
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74478
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2022 | The c.917G>A (p.R306H) alteration is located in exon 11 (coding exon 8) of the TMCO4 gene. This alteration results from a G to A substitution at nucleotide position 917, causing the arginine (R) at amino acid position 306 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