3-149767598-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001144960.3(ANKUB1):c.1064C>T(p.Pro355Leu) variant causes a missense change. The variant allele was found at a frequency of 0.00000214 in 1,399,388 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
ANKUB1
NM_001144960.3 missense
NM_001144960.3 missense
Scores
1
5
12
Clinical Significance
Conservation
PhyloP100: 6.88
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.19893733).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKUB1 | NM_001144960.3 | c.1064C>T | p.Pro355Leu | missense_variant | 5/6 | ENST00000446160.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKUB1 | ENST00000446160.7 | c.1064C>T | p.Pro355Leu | missense_variant | 5/6 | 5 | NM_001144960.3 | P1 | |
ANKUB1 | ENST00000484019.1 | c.*834C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/6 | 1 | ||||
ANKUB1 | ENST00000462519.3 | c.1064C>T | p.Pro355Leu | missense_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
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32
GnomAD3 exomes AF: 0.0000130 AC: 2AN: 154004Hom.: 0 AF XY: 0.0000245 AC XY: 2AN XY: 81718
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GnomAD4 exome AF: 0.00000214 AC: 3AN: 1399388Hom.: 0 Cov.: 34 AF XY: 0.00000290 AC XY: 2AN XY: 690204
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GnomAD4 genome Cov.: 32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.1064C>T (p.P355L) alteration is located in exon 5 (coding exon 5) of the ANKUB1 gene. This alteration results from a C to T substitution at nucleotide position 1064, causing the proline (P) at amino acid position 355 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
D;D;D
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
0.96
.;D
Vest4
MutPred
Gain of glycosylation at T353 (P = 0.0163);Gain of glycosylation at T353 (P = 0.0163);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
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