7-19772630-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001363562.2(TMEM196):c.67G>T(p.Val23Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000427 in 1,547,458 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001363562.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM196 | NM_001363562.2 | c.67G>T | p.Val23Leu | missense_variant | Exon 1 of 5 | ENST00000405844.6 | NP_001350491.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM196 | ENST00000405844.6 | c.67G>T | p.Val23Leu | missense_variant | Exon 1 of 5 | 5 | NM_001363562.2 | ENSP00000385087.2 | ||
TMEM196 | ENST00000405764.7 | c.67G>T | p.Val23Leu | missense_variant | Exon 1 of 4 | 1 | ENSP00000384234.3 | |||
TMEM196 | ENST00000422233.5 | c.-58+937G>T | intron_variant | Intron 1 of 4 | 5 | ENSP00000414247.1 | ||||
TMEM196 | ENST00000493519.2 | c.-58+472G>T | intron_variant | Intron 1 of 3 | 5 | ENSP00000438368.1 |
Frequencies
GnomAD3 genomes AF: 0.000224 AC: 34AN: 152070Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000529 AC: 8AN: 151154Hom.: 0 AF XY: 0.0000498 AC XY: 4AN XY: 80300
GnomAD4 exome AF: 0.0000229 AC: 32AN: 1395270Hom.: 0 Cov.: 31 AF XY: 0.0000247 AC XY: 17AN XY: 688110
GnomAD4 genome AF: 0.000223 AC: 34AN: 152188Hom.: 0 Cov.: 31 AF XY: 0.000255 AC XY: 19AN XY: 74400
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.67G>T (p.V23L) alteration is located in exon 1 (coding exon 1) of the TMEM196 gene. This alteration results from a G to T substitution at nucleotide position 67, causing the valine (V) at amino acid position 23 to be replaced by a leucine (L). 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