Genetic Variant KIF27:p.Ile1062Ile (chr9-83853800-A-T) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_017576.4(KIF27):c.3186T>A(p.Ile1062Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 1,611,514 control chromosomes in the GnomAD database, including 338,568 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.67 ( 35243 hom., cov: 31)

Exomes 𝑓: 0.64 ( 303325 hom. )

Consequence

KIF27
NM_017576.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.594

Variant links:

Genes affected

KIF27 (HGNC:18632): (kinesin family member 27) This gene is a member of the KIF27 (kinesin 4) sub-family of the mammalian kinesin family. The gene is an ortholog of the Drosophila Cos2 gene, which plays an important role in the Hedgehog signaling pathway. The encoded protein contains an N-terminal motor domain which includes nucleotide-binding and microtubule-interacting regions, a stalk domain containing a predicted coiled coil motif and a C-terminal tail domain. Alternatively spliced transcript variants have been observed for this gene. Pseudogenes associated with this gene are located on chromosome 9. [provided by RefSeq, Dec 2012]

KIF27 links:

ENSG00000231616 (HGNC:):

ENSG00000231616 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 9-83853800-A-T is Benign according to our data. Variant chr9-83853800-A-T is described in ClinVar as [Benign]. Clinvar id is 403012.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.594 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF27	NM_017576.4 link	c.3186T>A	p.Ile1062Ile	synonymous_variant	Exon 15 of 18	ENST00000297814.7	NP_060046.1	Q86VH2-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF27	ENST00000297814.7 link	c.3186T>A	p.Ile1062Ile	synonymous_variant	Exon 15 of 18	1	NM_017576.4	ENSP00000297814.2		Q86VH2-1

Frequencies

GnomAD3 genomes

AF:

0.673

AC:

102257

AN:

151916

Hom.:

35181

Cov.:

show subpopulations

Gnomad AFR

AF:

0.802

Gnomad AMI

AF:

0.576

Gnomad AMR

AF:

0.519

Gnomad ASJ

AF:

0.641

Gnomad EAS

AF:

0.519

Gnomad SAS

AF:

0.636

Gnomad FIN

AF:

0.694

Gnomad MID

AF:

0.668

Gnomad NFE

AF:

0.644

Gnomad OTH

AF:

0.648

GnomAD3 exomes

AF:

0.620

AC:

155598

AN:

250842

Hom.:

49845

AF XY:

0.628

AC XY:

85117

AN XY:

135576

show subpopulations

Gnomad AFR exome

AF:

0.806

Gnomad AMR exome

AF:

0.405

Gnomad ASJ exome

AF:

0.650

Gnomad EAS exome

AF:

0.506

Gnomad SAS exome

AF:

0.658

Gnomad FIN exome

AF:

0.693

Gnomad NFE exome

AF:

0.651

Gnomad OTH exome

AF:

0.621

GnomAD4 exome

AF:

0.642

AC:

936623

AN:

1459480

Hom.:

303325

Cov.:

AF XY:

0.642

AC XY:

466563

AN XY:

726214

show subpopulations

Gnomad4 AFR exome

AF:

0.813

Gnomad4 AMR exome

AF:

0.419

Gnomad4 ASJ exome

AF:

0.644

Gnomad4 EAS exome

AF:

0.531

Gnomad4 SAS exome

AF:

0.661

Gnomad4 FIN exome

AF:

0.699

Gnomad4 NFE exome

AF:

0.645

Gnomad4 OTH exome

AF:

0.646

GnomAD4 genome

AF:

0.673

AC:

102378

AN:

152034

Hom.:

35243

Cov.:

AF XY:

0.672

AC XY:

49949

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.803

Gnomad4 AMR

AF:

0.519

Gnomad4 ASJ

AF:

0.641

Gnomad4 EAS

AF:

0.519

Gnomad4 SAS

AF:

0.638

Gnomad4 FIN

AF:

0.694

Gnomad4 NFE

AF:

0.644

Gnomad4 OTH

AF:

0.651

Alfa

AF:

0.631

Hom.:

8041

Bravo

AF:

0.663

Asia WGS

AF:

0.595

AC:

2068

AN:

3478

EpiCase

AF:

0.641

EpiControl

AF:

0.646

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

7.2

DANN

Benign

0.78

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over