rs3803107
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000706.5(AVPR1A):c.*305C>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 0.191 in 273,904 control chromosomes in the GnomAD database, including 5,980 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 0.21 ( 4097 hom., cov: 33)
Exomes 𝑓: 0.16 ( 1883 hom. )
Consequence
AVPR1A
NM_000706.5 3_prime_UTR
NM_000706.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.593
Genes affected
AVPR1A (HGNC:895): (arginine vasopressin receptor 1A) The protein encoded by this gene acts as receptor for arginine vasopressin. This receptor belongs to the subfamily of G-protein coupled receptors which includes AVPR1B, V2R and OXT receptors. Its activity is mediated by G proteins which stimulate a phosphatidylinositol-calcium second messenger system. The receptor mediates cell contraction and proliferation, platelet aggregation, release of coagulation factor and glycogenolysis. [provided by RefSeq, 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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AVPR1A | NM_000706.5 | c.*305C>T | 3_prime_UTR_variant | 2/2 | ENST00000299178.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AVPR1A | ENST00000299178.4 | c.*305C>T | 3_prime_UTR_variant | 2/2 | 1 | NM_000706.5 | P1 | ||
AVPR1A | ENST00000550940.1 | c.538+367C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.212 AC: 32215AN: 151950Hom.: 4094 Cov.: 33
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GnomAD4 exome AF: 0.164 AC: 19969AN: 121836Hom.: 1883 Cov.: 3 AF XY: 0.165 AC XY: 10245AN XY: 62268
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GnomAD4 genome ? AF: 0.212 AC: 32239AN: 152068Hom.: 4097 Cov.: 33 AF XY: 0.209 AC XY: 15576AN XY: 74350
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ClinVar
Not reported inComputational scores
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Name
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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