3-42531500-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004624.4(VIPR1):c.820A>T(p.Thr274Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000694 in 1,440,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_004624.4 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 |
---|---|---|---|---|---|---|---|
VIPR1 | NM_004624.4 | c.820A>T | p.Thr274Ser | missense_variant | 8/13 | ENST00000325123.5 | |
VIPR1-AS1 | NR_046654.1 | n.118+521T>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VIPR1 | ENST00000325123.5 | c.820A>T | p.Thr274Ser | missense_variant | 8/13 | 1 | NM_004624.4 | P4 | |
VIPR1-AS1 | ENST00000452639.7 | n.743+521T>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.94e-7 AC: 1AN: 1440892Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1AN XY: 714636
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2024 | The c.820A>T (p.T274S) alteration is located in exon 8 (coding exon 8) of the VIPR1 gene. This alteration results from a A to T substitution at nucleotide position 820, causing the threonine (T) at amino acid position 274 to be replaced by a serine (S). 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