7-19772606-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001363562.2(TMEM196):c.91G>A(p.Val31Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000118 in 1,547,164 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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
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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.91G>A | p.Val31Ile | 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.91G>A | p.Val31Ile | missense_variant | Exon 1 of 5 | 5 | NM_001363562.2 | ENSP00000385087.2 | ||
TMEM196 | ENST00000405764.7 | c.91G>A | p.Val31Ile | missense_variant | Exon 1 of 4 | 1 | ENSP00000384234.3 | |||
TMEM196 | ENST00000422233.5 | c.-58+961G>A | intron_variant | Intron 1 of 4 | 5 | ENSP00000414247.1 | ||||
TMEM196 | ENST00000493519.2 | c.-58+496G>A | intron_variant | Intron 1 of 3 | 5 | ENSP00000438368.1 |
Frequencies
GnomAD3 genomes AF: 0.000559 AC: 85AN: 151924Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000160 AC: 24AN: 150110Hom.: 0 AF XY: 0.000113 AC XY: 9AN XY: 79822
GnomAD4 exome AF: 0.0000702 AC: 98AN: 1395122Hom.: 0 Cov.: 31 AF XY: 0.0000610 AC XY: 42AN XY: 688082
GnomAD4 genome AF: 0.000559 AC: 85AN: 152042Hom.: 0 Cov.: 31 AF XY: 0.000592 AC XY: 44AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.91G>A (p.V31I) alteration is located in exon 1 (coding exon 1) of the TMEM196 gene. This alteration results from a G to A substitution at nucleotide position 91, causing the valine (V) at amino acid position 31 to be replaced by an isoleucine (I). 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