chr12-63150082-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000706.5(AVPR1A):c.755C>T(p.Ala252Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000143 in 1,613,960 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000706.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AVPR1A | NM_000706.5 | c.755C>T | p.Ala252Val | missense_variant | 1/2 | ENST00000299178.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AVPR1A | ENST00000299178.4 | c.755C>T | p.Ala252Val | missense_variant | 1/2 | 1 | NM_000706.5 | P1 | |
AVPR1A | ENST00000550940.1 | c.98C>T | p.Ala33Val | missense_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152160Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000294 AC: 74AN: 251306Hom.: 1 AF XY: 0.000280 AC XY: 38AN XY: 135884
GnomAD4 exome AF: 0.000133 AC: 195AN: 1461800Hom.: 2 Cov.: 44 AF XY: 0.000113 AC XY: 82AN XY: 727212
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152160Hom.: 0 Cov.: 31 AF XY: 0.000229 AC XY: 17AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2021 | The c.755C>T (p.A252V) alteration is located in exon 1 (coding exon 1) of the AVPR1A gene. This alteration results from a C to T substitution at nucleotide position 755, causing the alanine (A) at amino acid position 252 to be replaced by a valine (V). 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