dbSNP rs2296225: KIF17:p.Ile341Val (chr1-20704549-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001122819.3(KIF17):c.1021A>G(p.Ile341Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0996 in 1,614,136 control chromosomes in the GnomAD database, including 10,393 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.098 ( 977 hom., cov: 32)

Exomes 𝑓: 0.10 ( 9416 hom. )

Consequence

KIF17
NM_001122819.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.49

Variant links:

Genes affected

KIF17 (HGNC:19167): (kinesin family member 17) Predicted to enable microtubule binding activity and plus-end-directed microtubule motor activity. Predicted to be involved in anterograde dendritic transport of neurotransmitter receptor complex and cell projection organization. Predicted to act upstream of or within microtubule-based process; protein-containing complex localization; and vesicle-mediated transport. Predicted to be located in microtubule cytoskeleton. Predicted to be part of intraciliary transport particle B and kinesin complex. Predicted to be active in cilium; microtubule cytoskeleton; and neuron projection. [provided by Alliance of Genome Resources, Apr 2022]

KIF17 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017932355).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF17	NM_001122819.3 link	c.1021A>G	p.Ile341Val	missense_variant	Exon 5 of 15	ENST00000400463.8	NP_001116291.1	Q9P2E2-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
KIF17	ENST00000400463.8 link	c.1021A>G	p.Ile341Val	missense_variant	Exon 5 of 15	1	NM_001122819.3	ENSP00000383311.3	Q9P2E2-3
KIF17	ENST00000247986.2 link	c.1021A>G	p.Ile341Val	missense_variant	Exon 5 of 15	1		ENSP00000247986.2	Q9P2E2-1
KIF17	ENST00000375044.5 link	c.721A>G	p.Ile241Val	missense_variant	Exon 5 of 15	1		ENSP00000364184.1	A0A0A0MRS8

Frequencies

GnomAD3 genomes

AF:

0.0982

AC:

14944

AN:

152136

Hom.:

982

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0985

Gnomad AMI

AF:

0.229

Gnomad AMR

AF:

0.0757

Gnomad ASJ

AF:

0.0562

Gnomad EAS

AF:

0.311

Gnomad SAS

AF:

0.254

Gnomad FIN

AF:

0.0425

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0847

Gnomad OTH

AF:

0.108

GnomAD3 exomes

AF:

0.118

AC:

29594

AN:

251444

Hom.:

2653

AF XY:

0.123

AC XY:

16660

AN XY:

135904

show subpopulations

Gnomad AFR exome

AF:

0.101

Gnomad AMR exome

AF:

0.0866

Gnomad ASJ exome

AF:

0.0543

Gnomad EAS exome

AF:

0.320

Gnomad SAS exome

AF:

0.247

Gnomad FIN exome

AF:

0.0410

Gnomad NFE exome

AF:

0.0834

Gnomad OTH exome

AF:

0.0974

GnomAD4 exome

AF:

0.0997

AC:

145801

AN:

1461882

Hom.:

9416

Cov.:

AF XY:

0.104

AC XY:

75720

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.0990

Gnomad4 AMR exome

AF:

0.0846

Gnomad4 ASJ exome

AF:

0.0561

Gnomad4 EAS exome

AF:

0.289

Gnomad4 SAS exome

AF:

0.242

Gnomad4 FIN exome

AF:

0.0430

Gnomad4 NFE exome

AF:

0.0860

Gnomad4 OTH exome

AF:

0.106

GnomAD4 genome

AF:

0.0981

AC:

14934

AN:

152254

Hom.:

977

Cov.:

AF XY:

0.101

AC XY:

7490

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.0985

Gnomad4 AMR

AF:

0.0757

Gnomad4 ASJ

AF:

0.0562

Gnomad4 EAS

AF:

0.310

Gnomad4 SAS

AF:

0.252

Gnomad4 FIN

AF:

0.0425

Gnomad4 NFE

AF:

0.0847

Gnomad4 OTH

AF:

0.105

Alfa

AF:

0.0915

Hom.:

1283

Bravo

AF:

0.100

TwinsUK

AF:

0.0895

AC:

332

ALSPAC

AF:

0.0916

AC:

353

ESP6500AA

AF:

0.0971

AC:

428

ESP6500EA

AF:

0.0837

AC:

720

ExAC

AF:

0.120

AC:

14585

Asia WGS

AF:

0.235

AC:

819

AN:

3478

EpiCase

AF:

0.0918

EpiControl

AF:

0.0852

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.095

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Benign

0.015

.;.;T

Eigen

Benign

-0.20

Eigen_PC

Benign

-0.0013

FATHMM_MKL

Uncertain

0.85

LIST_S2

Uncertain

0.94

D;T;T

MetaRNN

Benign

0.0018

T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

2.0

.;M;M

PrimateAI

Benign

0.46

PROVEAN

Benign

-0.83

N;N;N

REVEL

Benign

0.11

Sift

Benign

0.17

T;T;T

Sift4G

Benign

0.13

T;T;T

Polyphen

0.084, 0.050

.;B;B

Vest4

0.17

MPC

0.13

ClinPred

0.0094

GERP RS

5.3

Varity_R

0.051

gMVP

0.24

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over