7-150793995-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001101312.2(TMEM176B):c.281G>A(p.Ser94Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000675 in 1,613,690 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S94R) has been classified as Likely benign.
Frequency
Consequence
NM_001101312.2 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 |
---|---|---|---|---|---|---|---|---|
TMEM176B | NM_001101312.2 | c.281G>A | p.Ser94Asn | missense_variant | Exon 3 of 7 | ENST00000326442.10 | NP_001094782.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000878 AC: 22AN: 250550Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135356
GnomAD4 exome AF: 0.0000602 AC: 88AN: 1461384Hom.: 0 Cov.: 30 AF XY: 0.0000674 AC XY: 49AN XY: 727016
GnomAD4 genome AF: 0.000138 AC: 21AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.281G>A (p.S94N) alteration is located in exon 3 (coding exon 2) of the TMEM176B gene. This alteration results from a G to A substitution at nucleotide position 281, causing the serine (S) at amino acid position 94 to be replaced by an asparagine (N). 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