7-112775315-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_022484.6(TMEM168):āc.1132A>Gā(p.Thr378Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000583 in 1,612,284 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T378K) has been classified as Uncertain significance.
Frequency
Consequence
NM_022484.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM168 | NM_022484.6 | c.1132A>G | p.Thr378Ala | missense_variant | 3/5 | ENST00000312814.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM168 | ENST00000312814.11 | c.1132A>G | p.Thr378Ala | missense_variant | 3/5 | 1 | NM_022484.6 | P1 | |
LINC03076 | ENST00000656697.1 | n.469-121038T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249544Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134930
GnomAD4 exome AF: 0.0000623 AC: 91AN: 1460086Hom.: 0 Cov.: 31 AF XY: 0.0000441 AC XY: 32AN XY: 726290
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 28, 2023 | The c.1132A>G (p.T378A) alteration is located in exon 3 (coding exon 2) of the TMEM168 gene. This alteration results from a A to G substitution at nucleotide position 1132, causing the threonine (T) at amino acid position 378 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