rs2240191
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001143854.2(RPH3A):c.*1146G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 152,200 control chromosomes in the GnomAD database, including 6,230 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 0.26 ( 6230 hom., cov: 32)
Exomes 𝑓: 0.17 ( 0 hom. )
Consequence
RPH3A
NM_001143854.2 3_prime_UTR
NM_001143854.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.24
Genes affected
RPH3A (HGNC:17056): (rabphilin 3A) The protein encoded by this gene is thought to be an effector for RAB3A, which is a small G protein that acts in the late stages of neurotransmitter exocytosis. The encoded protein may be involved in neurotransmitter release and synaptic vesicle traffic. [provided by RefSeq, Dec 2016]
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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=-0.94).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPH3A | NM_001143854.2 | c.*1146G>T | 3_prime_UTR_variant | 22/22 | ENST00000389385.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPH3A | ENST00000389385.9 | c.*1146G>T | 3_prime_UTR_variant | 22/22 | 1 | NM_001143854.2 | P3 | ||
RPH3A | ENST00000549913.6 | n.4233G>T | non_coding_transcript_exon_variant | 14/14 | 1 | ||||
RPH3A | ENST00000415485.7 | c.*1146G>T | 3_prime_UTR_variant | 21/21 | 5 | P3 | |||
RPH3A | ENST00000549324.1 | n.1738G>T | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.263 AC: 40008AN: 151956Hom.: 6216 Cov.: 32
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GnomAD4 exome AF: 0.175 AC: 22AN: 126Hom.: 0 Cov.: 0 AF XY: 0.149 AC XY: 14AN XY: 94
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GnomAD4 genome ? AF: 0.263 AC: 40071AN: 152074Hom.: 6230 Cov.: 32 AF XY: 0.262 AC XY: 19450AN XY: 74338
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at