chr19-48333373-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_018273.4(TMEM143):c.1226A>C(p.Glu409Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000659 in 1,608,676 control chromosomes in the GnomAD database, including 3 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_018273.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM143 | NM_018273.4 | c.1226A>C | p.Glu409Ala | missense_variant | 8/8 | ENST00000293261.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM143 | ENST00000293261.8 | c.1226A>C | p.Glu409Ala | missense_variant | 8/8 | 1 | NM_018273.4 | P1 | |
TMEM143 | ENST00000377431.6 | c.926A>C | p.Glu309Ala | missense_variant | 6/6 | 1 | |||
TMEM143 | ENST00000435956.7 | c.1121A>C | p.Glu374Ala | missense_variant | 7/7 | 2 | |||
TMEM143 | ENST00000600816.1 | n.713A>C | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000137 AC: 34AN: 247414Hom.: 0 AF XY: 0.000172 AC XY: 23AN XY: 133946
GnomAD4 exome AF: 0.0000707 AC: 103AN: 1456412Hom.: 3 Cov.: 30 AF XY: 0.0000939 AC XY: 68AN XY: 724548
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.1226A>C (p.E409A) alteration is located in exon 8 (coding exon 8) of the TMEM143 gene. This alteration results from a A to C substitution at nucleotide position 1226, causing the glutamic acid (E) at amino acid position 409 to be replaced by an alanine (A). 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