chr1-206110265-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000707.5(AVPR1B):c.1199G>C(p.Arg400Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000707.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AVPR1B | NM_000707.5 | c.1199G>C | p.Arg400Thr | missense_variant | 2/2 | ENST00000367126.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AVPR1B | ENST00000367126.5 | c.1199G>C | p.Arg400Thr | missense_variant | 2/2 | 1 | NM_000707.5 | P1 | |
AVPR1B | ENST00000612906.1 | n.295G>C | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249594Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135412
GnomAD4 exome AF: 0.0000130 AC: 19AN: 1461776Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727202
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2022 | The c.1199G>C (p.R400T) alteration is located in exon 2 (coding exon 2) of the AVPR1B gene. This alteration results from a G to C substitution at nucleotide position 1199, causing the arginine (R) at amino acid position 400 to be replaced by a threonine (T). 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