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GeneBe

5-62348135-G-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_001098511.3(KIF2A):c.247G>T(p.Ala83Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A83T) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

KIF2A
NM_001098511.3 missense

Scores

1
18

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.101
Variant links:
Genes affected
KIF2A (HGNC:6318): (kinesin family member 2A) The protein encoded by this gene is a plus end-directed motor required for normal mitotic progression. The encoded protein is required for normal spindle activity during mitosis and is necessary for normal brain development. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
DIMT1 (HGNC:30217): (DIM1 rRNA methyltransferase and ribosome maturation factor) The protein encoded by this gene is a methyltransferase that is responsible for dimethylation of adjacent adenosines near the 18S rRNA decoding site. The encoded protein is essential for ribosome biogenesis, although its catalytic activity is not involved in the process. The yeast ortholog of this protein functions in the cytoplasm while this protein functions in the nucleus. [provided by RefSeq, Jan 2017]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.01576513).
BP6
Variant 5-62348135-G-T is Benign according to our data. Variant chr5-62348135-G-T is described in ClinVar as [Benign]. Clinvar id is 2782203.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KIF2ANM_001098511.3 linkuse as main transcriptc.247G>T p.Ala83Ser missense_variant 3/21 ENST00000407818.8
KIF2ANM_004520.5 linkuse as main transcriptc.247G>T p.Ala83Ser missense_variant 3/20
KIF2ANM_001243953.2 linkuse as main transcriptc.247G>T p.Ala83Ser missense_variant 3/20
KIF2ANM_001243952.2 linkuse as main transcriptc.166G>T p.Ala56Ser missense_variant 4/21

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KIF2AENST00000407818.8 linkuse as main transcriptc.247G>T p.Ala83Ser missense_variant 3/211 NM_001098511.3 A1O00139-4

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000756
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.00000824
AC:
1

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 submitterclinical testingInvitaeAug 17, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.067
BayesDel_addAF
Benign
-0.13
T
BayesDel_noAF
Benign
-0.42
Cadd
Benign
1.8
Dann
Benign
0.15
DEOGEN2
Benign
0.020
T;.;T;.;.;.
Eigen
Benign
-1.7
Eigen_PC
Benign
-1.7
FATHMM_MKL
Benign
0.076
N
LIST_S2
Uncertain
0.86
D;D;T;D;D;T
M_CAP
Benign
0.037
D
MetaRNN
Benign
0.016
T;T;T;T;T;T
MetaSVM
Benign
-0.92
T
MutationAssessor
Benign
-0.20
N;.;.;N;.;.
MutationTaster
Benign
1.0
N;N;N;N
PrimateAI
Benign
0.27
T
PROVEAN
Benign
0.19
N;N;N;N;N;N
REVEL
Benign
0.084
Sift
Benign
1.0
T;T;T;T;T;T
Sift4G
Benign
0.98
T;T;T;T;T;T
Polyphen
0.0
B;.;.;B;.;.
Vest4
0.19
MVP
0.57
MPC
0.78
ClinPred
0.016
T
GERP RS
-6.3
Varity_R
0.024
gMVP
0.16

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3194481; hg19: chr5-61643962; API