chr7-150804423-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_018487.3(TMEM176A):c.617C>T(p.Ser206Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,614,204 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018487.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM176A | NM_018487.3 | c.617C>T | p.Ser206Phe | missense_variant | Exon 6 of 7 | ENST00000004103.8 | NP_060957.2 | |
TMEM176A | XM_011516376.4 | c.668C>T | p.Ser223Phe | missense_variant | Exon 6 of 7 | XP_011514678.1 | ||
TMEM176A | XM_011516378.3 | c.607-404C>T | intron_variant | Intron 5 of 5 | XP_011514680.1 | |||
TMEM176A | XM_024446824.2 | c.556-404C>T | intron_variant | Intron 5 of 5 | XP_024302592.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251486Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135918
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461860Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727230
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152344Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74500
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.617C>T (p.S206F) alteration is located in exon 6 (coding exon 5) of the TMEM176A gene. This alteration results from a C to T substitution at nucleotide position 617, causing the serine (S) at amino acid position 206 to be replaced by a phenylalanine (F). 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