chr1-206110209-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000707.5(AVPR1B):c.1255G>A(p.Ala419Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000763 in 1,611,454 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 9/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000707.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AVPR1B | NM_000707.5 | c.1255G>A | p.Ala419Thr | missense_variant | 2/2 | ENST00000367126.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AVPR1B | ENST00000367126.5 | c.1255G>A | p.Ala419Thr | missense_variant | 2/2 | 1 | NM_000707.5 | P1 | |
AVPR1B | ENST00000612906.1 | n.351G>A | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000606 AC: 15AN: 247662Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134458
GnomAD4 exome AF: 0.0000644 AC: 94AN: 1459132Hom.: 0 Cov.: 32 AF XY: 0.0000662 AC XY: 48AN XY: 725308
GnomAD4 genome AF: 0.000190 AC: 29AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74494
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at