chr6-34994416-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_015245.3(ANKS1A):c.1417A>G(p.Thr473Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000913 in 1,611,988 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0045 ( 5 hom., cov: 32)
Exomes 𝑓: 0.00054 ( 4 hom. )
Consequence
ANKS1A
NM_015245.3 missense
NM_015245.3 missense
Scores
12
Clinical Significance
Conservation
PhyloP100: -0.00600
Genes affected
ANKS1A (HGNC:20961): (ankyrin repeat and sterile alpha motif domain containing 1A) Predicted to enable ephrin receptor binding activity. Predicted to be involved in ephrin receptor signaling pathway; neuron remodeling; and substrate-dependent cell migration. Predicted to act upstream of or within negative regulation of ubiquitin-dependent protein catabolic process and regulation of ephrin receptor signaling pathway. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, ANKS1A
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0038804114).
BP6
?
Variant 6-34994416-A-G is Benign according to our data. Variant chr6-34994416-A-G is described in ClinVar as [Benign]. Clinvar id is 768082.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 5 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ANKS1A | NM_015245.3 | c.1417A>G | p.Thr473Ala | missense_variant | 10/24 | ENST00000360359.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKS1A | ENST00000360359.5 | c.1417A>G | p.Thr473Ala | missense_variant | 10/24 | 1 | NM_015245.3 | ||
ANKS1A | ENST00000649117.1 | c.1480A>G | p.Thr494Ala | missense_variant | 11/25 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00451 AC: 687AN: 152230Hom.: 5 Cov.: 32
GnomAD3 genomes
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687
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GnomAD3 exomes AF: 0.00121 AC: 305AN: 251300Hom.: 2 AF XY: 0.000965 AC XY: 131AN XY: 135812
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GnomAD4 exome AF: 0.000535 AC: 781AN: 1459640Hom.: 4 Cov.: 33 AF XY: 0.000485 AC XY: 352AN XY: 726176
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GnomAD4 genome ? AF: 0.00453 AC: 690AN: 152348Hom.: 5 Cov.: 32 AF XY: 0.00424 AC XY: 316AN XY: 74506
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ExAC
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169
Asia WGS
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3478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 18, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
N;N
PrimateAI
Benign
T
Polyphen
0.0020
.;B
Vest4
0.17
MVP
0.26
MPC
0.32
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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