4-121669691-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001154.4(ANXA5):c.814G>A(p.Val272Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,611,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001154.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANXA5 | NM_001154.4 | c.814G>A | p.Val272Ile | missense_variant | 12/13 | ENST00000296511.10 | NP_001145.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANXA5 | ENST00000296511.10 | c.814G>A | p.Val272Ile | missense_variant | 12/13 | 1 | NM_001154.4 | ENSP00000296511.5 |
Frequencies
GnomAD3 genomes AF: 0.000107 AC: 16AN: 150076Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000240 AC: 6AN: 250478Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135394
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460834Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 726734
GnomAD4 genome AF: 0.000120 AC: 18AN: 150186Hom.: 0 Cov.: 31 AF XY: 0.000123 AC XY: 9AN XY: 73138
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.814G>A (p.V272I) alteration is located in exon 12 (coding exon 11) of the ANXA5 gene. This alteration results from a G to A substitution at nucleotide position 814, causing the valine (V) at amino acid position 272 to be replaced by an isoleucine (I). 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