chr20-16312412-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_024704.5(KIF16B):​c.3718G>T​(p.Ala1240Ser) 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. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 33)

Consequence

KIF16B
NM_024704.5 missense

Scores

18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.180
Variant links:
Genes affected
KIF16B (HGNC:15869): (kinesin family member 16B) The protein encoded by this gene is a kinesin-like protein that may be involved in intracellular trafficking. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2010]

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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=0.1729865).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KIF16BNM_024704.5 linkuse as main transcriptc.3718G>T p.Ala1240Ser missense_variant 25/26 ENST00000354981.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KIF16BENST00000354981.7 linkuse as main transcriptc.3718G>T p.Ala1240Ser missense_variant 25/261 NM_024704.5 P1Q96L93-1
KIF16BENST00000636835.1 linkuse as main transcriptc.3565G>T p.Ala1189Ser missense_variant 24/251

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
33

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 submitterclinical testingAmbry GeneticsApr 13, 2022The c.3718G>T (p.A1240S) alteration is located in exon 25 (coding exon 25) of the KIF16B gene. This alteration results from a G to T substitution at nucleotide position 3718, causing the alanine (A) at amino acid position 1240 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.074
BayesDel_addAF
Benign
-0.26
T
BayesDel_noAF
Benign
-0.62
CADD
Benign
15
DANN
Benign
0.96
DEOGEN2
Benign
0.043
T;T;.
Eigen
Benign
-0.65
Eigen_PC
Benign
-0.53
FATHMM_MKL
Benign
0.66
D
LIST_S2
Benign
0.85
T;D;T
M_CAP
Benign
0.051
D
MetaRNN
Benign
0.17
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.27
N;.;.
MutationTaster
Benign
0.69
D;D;N
PROVEAN
Benign
-0.89
N;.;.
REVEL
Benign
0.048
Sift
Benign
0.067
T;.;.
Sift4G
Benign
0.23
T;.;T
Polyphen
0.027
B;.;.
Vest4
0.079
MutPred
0.55
Gain of phosphorylation at A1240 (P = 0.0571);.;.;
MVP
0.24
ClinPred
0.093
T
GERP RS
1.1
Varity_R
0.20

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-16293057; API