4-950422-A-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_032326.4(TMEM175):āc.194A>Cā(p.Gln65Pro) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0918 in 1,611,220 control chromosomes in the GnomAD database, including 7,834 homozygotes. In-silico tool predicts a benign outcome for this variant. 10/14 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_032326.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM175 | NM_032326.4 | c.194A>C | p.Gln65Pro | missense_variant, splice_region_variant | 4/11 | ENST00000264771.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM175 | ENST00000264771.9 | c.194A>C | p.Gln65Pro | missense_variant, splice_region_variant | 4/11 | 1 | NM_032326.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0679 AC: 10336AN: 152196Hom.: 516 Cov.: 32
GnomAD3 exomes AF: 0.0703 AC: 17645AN: 251040Hom.: 891 AF XY: 0.0714 AC XY: 9684AN XY: 135698
GnomAD4 exome AF: 0.0943 AC: 137619AN: 1458906Hom.: 7318 Cov.: 30 AF XY: 0.0927 AC XY: 67282AN XY: 726034
GnomAD4 genome AF: 0.0679 AC: 10336AN: 152314Hom.: 516 Cov.: 32 AF XY: 0.0644 AC XY: 4797AN XY: 74484
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 19, 2019 | This variant is associated with the following publications: (PMID: 31658403, 30389748) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at