chr2-209653333-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001375505.1(MAP2):c.163G>A(p.Glu55Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0128 in 1,614,150 control chromosomes in the GnomAD database, including 155 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0092 ( 16 hom., cov: 32)
Exomes 𝑓: 0.013 ( 139 hom. )
Consequence
MAP2
NM_001375505.1 missense
NM_001375505.1 missense
Scores
2
6
9
Clinical Significance
Conservation
PhyloP100: 6.82
Genes affected
MAP2 (HGNC:6839): (microtubule associated protein 2) This gene encodes a protein that belongs to the microtubule-associated protein family. The proteins of this family are thought to be involved in microtubule assembly, which is an essential step in neurogenesis. The products of similar genes in rat and mouse are neuron-specific cytoskeletal proteins that are enriched in dentrites, implicating a role in determining and stabilizing dentritic shape during neuron development. A number of alternatively spliced variants encoding distinct isoforms have been described. [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0052931905).
BP6
?
Variant 2-209653333-G-A is Benign according to our data. Variant chr2-209653333-G-A is described in ClinVar as [Benign]. Clinvar id is 774414.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4_exome allele frequency = 0.0131 (19208/1461820) while in subpopulation NFE AF= 0.0154 (17150/1111970). AF 95% confidence interval is 0.0152. There are 139 homozygotes in gnomad4_exome. There are 9374 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1395 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP2 | NM_001375505.1 | c.163G>A | p.Glu55Lys | missense_variant | 5/16 | ENST00000682079.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP2 | ENST00000682079.1 | c.163G>A | p.Glu55Lys | missense_variant | 5/16 | NM_001375505.1 |
Frequencies
GnomAD3 genomes ? AF: 0.00916 AC: 1395AN: 152212Hom.: 16 Cov.: 32
GnomAD3 genomes
?
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1395
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GnomAD3 exomes AF: 0.00922 AC: 2316AN: 251248Hom.: 18 AF XY: 0.00952 AC XY: 1292AN XY: 135776
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GnomAD4 exome AF: 0.0131 AC: 19208AN: 1461820Hom.: 139 Cov.: 32 AF XY: 0.0129 AC XY: 9374AN XY: 727210
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GnomAD4 genome ? AF: 0.00916 AC: 1395AN: 152330Hom.: 16 Cov.: 32 AF XY: 0.00885 AC XY: 659AN XY: 74484
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51
ESP6500AA
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10
ESP6500EA
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109
ExAC
?
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1136
Asia WGS
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6
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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 | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Pathogenic
Dann
Pathogenic
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;.;D;D;D
MetaRNN
Benign
T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.;M;M;.;M;M
MutationTaster
Benign
D;D;D;N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;D;N;N;D;N;N
REVEL
Benign
Sift
Uncertain
D;D;D;D;D;D;D
Sift4G
Benign
T;T;D;T;D;T;D
Polyphen
1.0, 0.83, 0.61
.;.;D;P;P;P;D
Vest4
MVP
MPC
0.22
ClinPred
T
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