12-69655784-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032735.3(BEST3):c.1130A>G(p.Glu377Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0000341 in 1,610,724 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E377A) has been classified as Uncertain significance.
Frequency
Consequence
NM_032735.3 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 |
---|---|---|---|---|---|---|---|
BEST3 | NM_032735.3 | c.1130A>G | p.Glu377Gly | missense_variant | 10/10 | ENST00000330891.10 | |
LOC105369823 | XR_007063357.1 | n.311+16770T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BEST3 | ENST00000330891.10 | c.1130A>G | p.Glu377Gly | missense_variant | 10/10 | 5 | NM_032735.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152040Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000892 AC: 22AN: 246636Hom.: 0 AF XY: 0.0000672 AC XY: 9AN XY: 133964
GnomAD4 exome AF: 0.0000357 AC: 52AN: 1458566Hom.: 0 Cov.: 34 AF XY: 0.0000386 AC XY: 28AN XY: 724998
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152158Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.1130A>G (p.E377G) alteration is located in exon 10 (coding exon 9) of the BEST3 gene. This alteration results from a A to G substitution at nucleotide position 1130, causing the glutamic acid (E) at amino acid position 377 to be replaced by a glycine (G). 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