Variant rs74436006 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000297814.7(KIF27):c.3054A>G(p.Glu1018=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0149 in 1,612,906 control chromosomes in the GnomAD database, including 276 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.023 ( 66 hom., cov: 31)

Exomes 𝑓: 0.014 ( 210 hom. )

Consequence

KIF27
ENST00000297814.7 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0390

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:

(HGNC:):

links:

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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 9-83859252-T-C is Benign according to our data. Variant chr9-83859252-T-C is described in ClinVar as [Benign]. Clinvar id is 403014.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.039 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF27	NM_017576.4 linkuse as main transcript	c.3054A>G	p.Glu1018=	synonymous_variant	14/18	ENST00000297814.7	NP_060046.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF27	ENST00000297814.7 linkuse as main transcript	c.3054A>G	p.Glu1018=	synonymous_variant	14/18	1	NM_017576.4	ENSP00000297814	P1	Q86VH2-1
	ENST00000591217.5 linkuse as main transcript	n.880-26T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0232

AC:

3530

AN:

151908

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0527

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.0143

Gnomad ASJ

AF:

0.0323

Gnomad EAS

AF:

0.000962

Gnomad SAS

AF:

0.0166

Gnomad FIN

AF:

0.00668

Gnomad MID

AF:

0.0159

Gnomad NFE

AF:

0.0120

Gnomad OTH

AF:

0.0182

GnomAD3 exomes

AF:

0.0150

AC:

3757

AN:

251290

Hom.:

AF XY:

0.0147

AC XY:

1996

AN XY:

135836

show subpopulations

Gnomad AFR exome

AF:

0.0512

Gnomad AMR exome

AF:

0.00761

Gnomad ASJ exome

AF:

0.0364

Gnomad EAS exome

AF:

0.000326

Gnomad SAS exome

AF:

0.0191

Gnomad FIN exome

AF:

0.00517

Gnomad NFE exome

AF:

0.0133

Gnomad OTH exome

AF:

0.0145

GnomAD4 exome

AF:

0.0140

AC:

20485

AN:

1460882

Hom.:

210

Cov.:

AF XY:

0.0143

AC XY:

10406

AN XY:

726778

show subpopulations

Gnomad4 AFR exome

AF:

0.0511

Gnomad4 AMR exome

AF:

0.00814

Gnomad4 ASJ exome

AF:

0.0359

Gnomad4 EAS exome

AF:

0.000428

Gnomad4 SAS exome

AF:

0.0191

Gnomad4 FIN exome

AF:

0.00453

Gnomad4 NFE exome

AF:

0.0130

Gnomad4 OTH exome

AF:

0.0171

GnomAD4 genome

AF:

0.0232

AC:

3532

AN:

152024

Hom.:

Cov.:

AF XY:

0.0228

AC XY:

1698

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.0526

Gnomad4 AMR

AF:

0.0142

Gnomad4 ASJ

AF:

0.0323

Gnomad4 EAS

AF:

0.000965

Gnomad4 SAS

AF:

0.0166

Gnomad4 FIN

AF:

0.00668

Gnomad4 NFE

AF:

0.0120

Gnomad4 OTH

AF:

0.0180

Alfa

AF:

0.0193

Hom.:

Bravo

AF:

0.0255

Asia WGS

AF:

0.0100

AC:

AN:

3478

EpiCase

AF:

0.0133

EpiControl

AF:

0.0160

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 29, 2016

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: MAF -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

3.4

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