18-9254826-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015208.5(ANKRD12):āc.1559A>Gā(p.Asn520Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000749 in 1,334,962 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_015208.5 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 |
---|---|---|---|---|---|---|---|---|
ANKRD12 | NM_015208.5 | c.1559A>G | p.Asn520Ser | missense_variant | 9/13 | ENST00000262126.9 | NP_056023.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ANKRD12 | ENST00000262126.9 | c.1559A>G | p.Asn520Ser | missense_variant | 9/13 | 1 | NM_015208.5 | ENSP00000262126 | P4 | |
ANKRD12 | ENST00000400020.7 | c.1490A>G | p.Asn497Ser | missense_variant | 8/12 | 1 | ENSP00000382897 | A2 | ||
ANKRD12 | ENST00000359158.7 | c.*673A>G | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 2 | ENSP00000352073 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 7.49e-7 AC: 1AN: 1334962Hom.: 0 Cov.: 33 AF XY: 0.00000153 AC XY: 1AN XY: 654002
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | The c.1559A>G (p.N520S) alteration is located in exon 9 (coding exon 8) of the ANKRD12 gene. This alteration results from a A to G substitution at nucleotide position 1559, causing the asparagine (N) at amino acid position 520 to be replaced by a serine (S). 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