chr1-206116113-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000707.5(AVPR1B):c.778C>T(p.Arg260Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,614,204 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/11 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.778C>T | p.Arg260Trp | missense_variant | 1/2 | ENST00000367126.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AVPR1B | ENST00000367126.5 | c.778C>T | p.Arg260Trp | missense_variant | 1/2 | 1 | NM_000707.5 | P1 | |
AVPR1B | ENST00000612906.1 | n.36+1551C>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250904Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135716
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461868Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727236
GnomAD4 genome ? AF: 0.00000656 AC: 1AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 30, 2023 | The c.778C>T (p.R260W) alteration is located in exon 1 (coding exon 1) of the AVPR1B gene. This alteration results from a C to T substitution at nucleotide position 778, causing the arginine (R) at amino acid position 260 to be replaced by a tryptophan (W). 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