chrX-79171081-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_032553.3(GPR174):c.74C>T(p.Thr25Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,203,667 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032553.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPR174 | NM_032553.3 | c.74C>T | p.Thr25Ile | missense_variant | Exon 3 of 3 | ENST00000645147.2 | NP_115942.1 | |
GPR174 | XM_047442579.1 | c.74C>T | p.Thr25Ile | missense_variant | Exon 3 of 3 | XP_047298535.1 | ||
GPR174 | XM_047442580.1 | c.74C>T | p.Thr25Ile | missense_variant | Exon 2 of 2 | XP_047298536.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000267 AC: 3AN: 112232Hom.: 0 Cov.: 23 AF XY: 0.0000582 AC XY: 2AN XY: 34392
GnomAD3 exomes AF: 0.0000388 AC: 7AN: 180520Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 65524
GnomAD4 exome AF: 0.0000101 AC: 11AN: 1091379Hom.: 0 Cov.: 31 AF XY: 0.0000112 AC XY: 4AN XY: 357063
GnomAD4 genome AF: 0.0000267 AC: 3AN: 112288Hom.: 0 Cov.: 23 AF XY: 0.0000580 AC XY: 2AN XY: 34458
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.74C>T (p.T25I) alteration is located in exon 1 (coding exon 1) of the GPR174 gene. This alteration results from a C to T substitution at nucleotide position 74, causing the threonine (T) at amino acid position 25 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