dbSNP rs193920855: KIF16B:p.Val530Leu (chr20-16427128-C-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_024704.5(KIF16B):c.1588G>T(p.Val530Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,456,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V530M) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

KIF16B
NM_024704.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.286

Publications

0 publications found

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]

KIF16B links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.08679718).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF16B	NM_024704.5 link	c.1588G>T	p.Val530Leu	missense_variant	Exon 15 of 26	ENST00000354981.7	NP_078980.3	Q96L93-1A0A140VK74

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
KIF16B	ENST00000354981.7 link	c.1588G>T	p.Val530Leu	missense_variant	Exon 15 of 26	1	NM_024704.5	ENSP00000347076.2	Q96L93-1
KIF16B	ENST00000408042.5 link	c.1588G>T	p.Val530Leu	missense_variant	Exon 15 of 23	1		ENSP00000384164.1	Q96L93-2
KIF16B	ENST00000636835.1 link	c.1588G>T	p.Val530Leu	missense_variant	Exon 15 of 25	1		ENSP00000489838.1	A0A1B0GTU3
KIF16B	ENST00000635823.2 link	c.1588G>T	p.Val530Leu	missense_variant	Exon 15 of 23	5		ENSP00000490639.2	A0A1B0GVS8

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.87e-7

AC:

AN:

1456130

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

724150

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33258

American (AMR)

AF:

0.00

AC:

AN:

44042

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25986

East Asian (EAS)

AF:

0.00

AC:

AN:

39562

South Asian (SAS)

AF:

0.0000118

AC:

AN:

84872

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53280

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5742

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1109244

Other (OTH)

AF:

0.00

AC:

AN:

60144

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.068

BayesDel_addAF

Benign

-0.19

BayesDel_noAF

Benign

-0.51

CADD

Benign

2.2

(source)

DANN

Benign

0.90

DEOGEN2

Benign

0.14

T;T;.

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.070

LIST_S2

Benign

0.68

T;T;T

M_CAP

Benign

0.062

MetaRNN

Benign

0.087

T;T;T

MetaSVM

Benign

-0.85

MutationAssessor

Benign

0.10

N;.;N

PhyloP100

-0.29

PrimateAI

Benign

0.26

PROVEAN

Benign

-0.71

N;.;N

REVEL

Benign

0.24

Sift

Benign

0.077

T;.;T

Sift4G

Benign

0.30

T;.;T

Polyphen

0.0

B;.;B

Vest4

0.043

MutPred

0.54

Loss of catalytic residue at V530 (P = 0.0338);Loss of catalytic residue at V530 (P = 0.0338);Loss of catalytic residue at V530 (P = 0.0338);

MVP

0.48

MPC

0.11

ClinPred

0.070

GERP RS

-4.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.075

gMVP

0.32

Mutation Taster

=98/2

polymorphism

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over