chr4-168181734-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_007193.5(ANXA10):c.776C>T(p.Ala259Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000164 in 1,585,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007193.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANXA10 | ENST00000359299.8 | c.776C>T | p.Ala259Val | missense_variant | Exon 10 of 12 | 1 | NM_007193.5 | ENSP00000352248.3 | ||
ANXA10 | ENST00000507278.5 | n.439C>T | non_coding_transcript_exon_variant | Exon 5 of 7 | 1 | |||||
ENSG00000287188 | ENST00000654434.1 | n.466-9456G>A | intron_variant | Intron 1 of 1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152094Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248672Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134634
GnomAD4 exome AF: 0.0000161 AC: 23AN: 1432996Hom.: 0 Cov.: 27 AF XY: 0.0000210 AC XY: 15AN XY: 714626
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152094Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.776C>T (p.A259V) alteration is located in exon 10 (coding exon 10) of the ANXA10 gene. This alteration results from a C to T substitution at nucleotide position 776, causing the alanine (A) at amino acid position 259 to be replaced by a valine (V). 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