chr7-19722082-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001366626.1(TMEM196):c.530G>A(p.Arg177Lys) 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. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001366626.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM196 | NM_001363562.2 | c.*46G>A | 3_prime_UTR_variant | Exon 5 of 5 | ENST00000405844.6 | NP_001350491.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM196 | ENST00000405764.7 | c.512G>A | p.Arg171Lys | missense_variant | Exon 4 of 4 | 1 | ENSP00000384234.3 | |||
TMEM196 | ENST00000405844 | c.*46G>A | 3_prime_UTR_variant | Exon 5 of 5 | 5 | NM_001363562.2 | ENSP00000385087.2 | |||
TMEM196 | ENST00000493519.2 | c.308G>A | p.Arg103Lys | missense_variant | Exon 4 of 4 | 5 | ENSP00000438368.1 | |||
TMEM196 | ENST00000422233 | c.*46G>A | 3_prime_UTR_variant | Exon 5 of 5 | 5 | ENSP00000414247.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1457730Hom.: 0 Cov.: 29 AF XY: 0.00 AC XY: 0AN XY: 725264
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.512G>A (p.R171K) alteration is located in exon 4 (coding exon 4) of the TMEM196 gene. This alteration results from a G to A substitution at nucleotide position 512, causing the arginine (R) at amino acid position 171 to be replaced by a lysine (K). 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