12-56243222-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_173595.4(ANKRD52):c.3151G>A(p.Ala1051Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000682 in 1,613,520 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173595.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ANKRD52 | NM_173595.4 | c.3151G>A | p.Ala1051Thr | missense_variant | Exon 28 of 28 | ENST00000267116.8 | NP_775866.2 | |
ANKRD52 | XM_017019183.2 | c.3148G>A | p.Ala1050Thr | missense_variant | Exon 27 of 27 | XP_016874672.1 | ||
ANKRD52 | XM_011538197.3 | c.2968G>A | p.Ala990Thr | missense_variant | Exon 27 of 27 | XP_011536499.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000122 AC: 3AN: 245534Hom.: 0 AF XY: 0.00000746 AC XY: 1AN XY: 133994
GnomAD4 exome AF: 0.0000671 AC: 98AN: 1461174Hom.: 0 Cov.: 32 AF XY: 0.0000674 AC XY: 49AN XY: 726874
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152346Hom.: 0 Cov.: 32 AF XY: 0.0000805 AC XY: 6AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3151G>A (p.A1051T) alteration is located in exon 28 (coding exon 28) of the ANKRD52 gene. This alteration results from a G to A substitution at nucleotide position 3151, causing the alanine (A) at amino acid position 1051 to be replaced by a threonine (T). 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