chr4-78573220-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005139.3(ANXA3):c.56G>A(p.Ser19Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00268 in 1,613,618 control chromosomes in the GnomAD database, including 115 homozygotes. 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 Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S19R) has been classified as Uncertain significance.
Frequency
Consequence
NM_005139.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANXA3 | NM_005139.3 | c.56G>A | p.Ser19Asn | missense_variant | 3/13 | ENST00000264908.11 | |
ANXA3 | XM_047450154.1 | c.56G>A | p.Ser19Asn | missense_variant | 3/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANXA3 | ENST00000264908.11 | c.56G>A | p.Ser19Asn | missense_variant | 3/13 | 1 | NM_005139.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0139 AC: 2113AN: 152154Hom.: 53 Cov.: 32
GnomAD3 exomes AF: 0.00377 AC: 946AN: 251050Hom.: 25 AF XY: 0.00282 AC XY: 382AN XY: 135674
GnomAD4 exome AF: 0.00150 AC: 2190AN: 1461346Hom.: 60 Cov.: 30 AF XY: 0.00135 AC XY: 984AN XY: 726978
GnomAD4 genome ? AF: 0.0140 AC: 2130AN: 152272Hom.: 55 Cov.: 32 AF XY: 0.0132 AC XY: 980AN XY: 74464
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at