GeneBe

rs522444

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000490550.2(KIFAP3):​c.77+10272C>T variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

KIFAP3
ENST00000490550.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.243

Publications

10 publications found
Variant links:
Genes affected
KIFAP3 (HGNC:17060): (kinesin associated protein 3) The small G protein GDP dissociation stimulator (smg GDS) is a regulator protein having two activities on a group of small G proteins including the Rho and Rap1 family members and Ki-Ras; one is to stimulate their GDP/GTP exchange reactions, and the other is to inhibit their interactions with membranes. The protein encoded by this gene contains 9 'Armadillo' repeats and interacts with the smg GDS protein through these repeats. This protein, which is highly concentrated around the endoplasmic reticulum, is phosphorylated by v-src, and this phosphorylation reduces the affinity of the protein for smg GDS. It is thought that this protein serves as a linker between human chromosome-associated polypeptide (HCAP) and KIF3A/B, a kinesin superfamily protein in the nucleus, and that it plays a role in the interaction of chromosomes with an ATPase motor protein. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2011]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000490550.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
KIFAP3
NM_014970.4
MANE Select
c.-296C>T
upstream_gene
N/ANP_055785.2
KIFAP3
NM_001375830.1
c.-296C>T
upstream_gene
N/ANP_001362759.1
KIFAP3
NM_001375831.1
c.-296C>T
upstream_gene
N/ANP_001362760.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
KIFAP3
ENST00000490550.2
TSL:5
c.77+10272C>T
intron
N/AENSP00000518914.1A0AAQ5BGI3
KIFAP3
ENST00000361580.7
TSL:1 MANE Select
c.-296C>T
upstream_gene
N/AENSP00000354560.2Q92845-1
KIFAP3
ENST00000367767.5
TSL:1
c.-296C>T
upstream_gene
N/AENSP00000356741.1Q92845-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1098792
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
523312
African (AFR)
AF:
0.00
AC:
0
AN:
25106
American (AMR)
AF:
0.00
AC:
0
AN:
15128
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
13842
East Asian (EAS)
AF:
0.00
AC:
0
AN:
24056
South Asian (SAS)
AF:
0.00
AC:
0
AN:
41116
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
16740
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
2844
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
916900
Other (OTH)
AF:
0.00
AC:
0
AN:
43060
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
8.7
DANN
Benign
0.96
PhyloP100
0.24
PromoterAI
0.0014
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs522444; hg19: chr1-170043904; API