5-151109759-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001155.5(ANXA6):c.1678C>T(p.Arg560Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000746 in 1,608,024 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_001155.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANXA6 | NM_001155.5 | c.1678C>T | p.Arg560Trp | missense_variant | Exon 22 of 26 | ENST00000354546.10 | NP_001146.2 | |
ANXA6 | NM_001363114.2 | c.1660C>T | p.Arg554Trp | missense_variant | Exon 21 of 25 | NP_001350043.1 | ||
ANXA6 | NM_001193544.2 | c.1582C>T | p.Arg528Trp | missense_variant | Exon 21 of 25 | NP_001180473.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000687 AC: 10AN: 1455862Hom.: 0 Cov.: 30 AF XY: 0.00000414 AC XY: 3AN XY: 723888
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1678C>T (p.R560W) alteration is located in exon 22 (coding exon 21) of the ANXA6 gene. This alteration results from a C to T substitution at nucleotide position 1678, causing the arginine (R) at amino acid position 560 to be replaced by a tryptophan (W). 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