4-78601545-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005139.3(ANXA3):c.766G>A(p.Glu256Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000595 in 1,613,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005139.3 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 |
---|---|---|---|---|---|---|---|
ANXA3 | NM_005139.3 | c.766G>A | p.Glu256Lys | missense_variant | 11/13 | ENST00000264908.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANXA3 | ENST00000264908.11 | c.766G>A | p.Glu256Lys | missense_variant | 11/13 | 1 | NM_005139.3 | P1 | |
ANXA3 | ENST00000503570.6 | c.649G>A | p.Glu217Lys | missense_variant | 12/14 | 5 | |||
ANXA3 | ENST00000512884.5 | c.649G>A | p.Glu217Lys | missense_variant | 10/12 | 5 | |||
ANXA3 | ENST00000505805.1 | n.378G>A | non_coding_transcript_exon_variant | 2/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 251214Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135768
GnomAD4 exome AF: 0.0000636 AC: 93AN: 1461646Hom.: 0 Cov.: 30 AF XY: 0.0000591 AC XY: 43AN XY: 727132
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 05, 2023 | The c.766G>A (p.E256K) alteration is located in exon 11 (coding exon 10) of the ANXA3 gene. This alteration results from a G to A substitution at nucleotide position 766, causing the glutamic acid (E) at amino acid position 256 to be replaced by a lysine (K). 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