rs121918287
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM1PP3PP5BS2_Supporting
The NM_004183.4(BEST1):c.949G>A(p.Val317Met) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000144 in 1,461,522 control chromosomes in the GnomAD database, with no homozygous occurrence. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V317L) has been classified as Uncertain significance.
Frequency
Consequence
NM_004183.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BEST1 | NM_004183.4 | c.949G>A | p.Val317Met | missense_variant, splice_region_variant | 9/11 | ENST00000378043.9 | |
LOC107984334 | XR_001748245.2 | n.1C>T | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BEST1 | ENST00000378043.9 | c.949G>A | p.Val317Met | missense_variant, splice_region_variant | 9/11 | 1 | NM_004183.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461522Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727004
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Autosomal recessive bestrophinopathy Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2008 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at