rs2117975
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007223.3(GPR176):c.172+54742C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,070 control chromosomes in the GnomAD database, including 1,188 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.12 ( 1188 hom., cov: 32)
Consequence
GPR176
NM_007223.3 intron
NM_007223.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.45
Genes affected
GPR176 (HGNC:32370): (G protein-coupled receptor 176) Members of the G protein-coupled receptor family, such as GPR176, are cell surface receptors involved in responses to hormones, growth factors, and neurotransmitters (Hata et al., 1995 [PubMed 7893747]).[supplied by OMIM, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.05).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPR176 | NM_007223.3 | c.172+54742C>T | intron_variant | ENST00000561100.2 | |||
GPR176 | NM_001271854.2 | c.172+54742C>T | intron_variant | ||||
GPR176 | XM_017021878.3 | c.-65+54742C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPR176 | ENST00000561100.2 | c.172+54742C>T | intron_variant | 1 | NM_007223.3 | P1 | |||
GPR176 | ENST00000299092.4 | c.172+54742C>T | intron_variant | 1 | |||||
GPR176 | ENST00000558041.5 | n.98-4191C>T | intron_variant, non_coding_transcript_variant | 3 | |||||
GPR176 | ENST00000560729.1 | n.73-2694C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.119 AC: 18126AN: 151952Hom.: 1192 Cov.: 32
GnomAD3 genomes
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151952
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.119 AC: 18133AN: 152070Hom.: 1188 Cov.: 32 AF XY: 0.117 AC XY: 8673AN XY: 74356
GnomAD4 genome
?
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18133
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152070
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32
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8673
AN XY:
74356
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402
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3472
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at