rs1114591
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015208.5(ANKRD12):c.*4700T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,112 control chromosomes in the GnomAD database, including 4,114 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.21 ( 4114 hom., cov: 32)
Exomes 𝑓: 0.13 ( 0 hom. )
Consequence
ANKRD12
NM_015208.5 3_prime_UTR
NM_015208.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.301
Genes affected
ANKRD12 (HGNC:29135): (ankyrin repeat domain 12) This gene encodes a member of the ankyrin repeats-containing cofactor family. These proteins may inhibit the transcriptional activity of nuclear receptors through the recruitment of histone deacetylases. The encoded protein interacts with p160 coactivators and also represses transcription mediated by the coactivator alteration/deficiency in activation 3 (ADA3). Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKRD12 | NM_015208.5 | c.*4700T>C | 3_prime_UTR_variant | 13/13 | ENST00000262126.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKRD12 | ENST00000262126.9 | c.*4700T>C | 3_prime_UTR_variant | 13/13 | 1 | NM_015208.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.209 AC: 31800AN: 151986Hom.: 4095 Cov.: 32
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GnomAD4 exome AF: 0.125 AC: 1AN: 8Hom.: 0 Cov.: 0 AF XY: 0.167 AC XY: 1AN XY: 6
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GnomAD4 genome ? AF: 0.209 AC: 31856AN: 152104Hom.: 4114 Cov.: 32 AF XY: 0.202 AC XY: 15015AN XY: 74368
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at