6-39343778-C-T

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2

The NM_145027.6(KIF6):​c.2359G>A​(p.Gly787Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00387 in 1,612,614 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0029 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0040 ( 20 hom. )

Consequence

KIF6
NM_145027.6 missense

Scores

4
11
4

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 4.19
Variant links:
Genes affected
KIF6 (HGNC:21202): (kinesin family member 6) This gene encodes a member of a family of molecular motors which are involved in intracellular transport of protein complexes, membrane organelles, and messenger ribonucleic acid along microtubules. Kinesins function as homodimeric molecules with two N-terminal head domains that move along microtubules and two C-terminal tail domains that interact with the transported cargo, either directly or indirectly, through adapter molecules. This gene is ubiquitously expressed in coronary arteries and other vascular tissue. A naturally occurring mutation in this gene is associated with coronary heart disease. [provided by RefSeq, May 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.031724036).
BP6
Variant 6-39343778-C-T is Benign according to our data. Variant chr6-39343778-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3056494.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High Homozygotes in GnomAdExome4 at 20 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KIF6NM_145027.6 linkc.2359G>A p.Gly787Arg missense_variant 22/23 ENST00000287152.12 NP_659464.3 Q6ZMV9-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KIF6ENST00000287152.12 linkc.2359G>A p.Gly787Arg missense_variant 22/232 NM_145027.6 ENSP00000287152.7 Q6ZMV9-1

Frequencies

GnomAD3 genomes
AF:
0.00294
AC:
447
AN:
152206
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000893
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00294
Gnomad ASJ
AF:
0.00231
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00245
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00482
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.00212
AC:
529
AN:
249594
Hom.:
1
AF XY:
0.00210
AC XY:
283
AN XY:
134880
show subpopulations
Gnomad AFR exome
AF:
0.000924
Gnomad AMR exome
AF:
0.000790
Gnomad ASJ exome
AF:
0.00160
Gnomad EAS exome
AF:
0.0000546
Gnomad SAS exome
AF:
0.0000330
Gnomad FIN exome
AF:
0.00162
Gnomad NFE exome
AF:
0.00379
Gnomad OTH exome
AF:
0.000989
GnomAD4 exome
AF:
0.00397
AC:
5792
AN:
1460290
Hom.:
20
Cov.:
30
AF XY:
0.00380
AC XY:
2761
AN XY:
726402
show subpopulations
Gnomad4 AFR exome
AF:
0.000628
Gnomad4 AMR exome
AF:
0.000811
Gnomad4 ASJ exome
AF:
0.00165
Gnomad4 EAS exome
AF:
0.000151
Gnomad4 SAS exome
AF:
0.0000116
Gnomad4 FIN exome
AF:
0.00150
Gnomad4 NFE exome
AF:
0.00476
Gnomad4 OTH exome
AF:
0.00514
GnomAD4 genome
AF:
0.00293
AC:
447
AN:
152324
Hom.:
1
Cov.:
32
AF XY:
0.00271
AC XY:
202
AN XY:
74472
show subpopulations
Gnomad4 AFR
AF:
0.000890
Gnomad4 AMR
AF:
0.00294
Gnomad4 ASJ
AF:
0.00231
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00245
Gnomad4 NFE
AF:
0.00482
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.00363
Hom.:
4
Bravo
AF:
0.00250
TwinsUK
AF:
0.00297
AC:
11
ALSPAC
AF:
0.00234
AC:
9
ESP6500AA
AF:
0.00204
AC:
9
ESP6500EA
AF:
0.00488
AC:
42
ExAC
AF:
0.00212
AC:
257
EpiCase
AF:
0.00409
EpiControl
AF:
0.00452

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

KIF6-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesFeb 10, 2022This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.60
BayesDel_addAF
Benign
-0.096
T
BayesDel_noAF
Uncertain
0.090
CADD
Pathogenic
31
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.062
T;.;.;.
Eigen
Uncertain
0.59
Eigen_PC
Uncertain
0.54
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Uncertain
0.91
D;D;D;D
M_CAP
Uncertain
0.15
D
MetaRNN
Benign
0.032
T;T;T;T
MetaSVM
Uncertain
0.64
D
MutationAssessor
Uncertain
2.4
M;.;.;.
PrimateAI
Uncertain
0.62
T
PROVEAN
Pathogenic
-4.4
D;D;D;.
REVEL
Uncertain
0.56
Sift
Pathogenic
0.0
D;D;D;.
Sift4G
Uncertain
0.0040
D;D;D;D
Polyphen
1.0
D;.;.;.
Vest4
0.59
MutPred
0.26
Gain of phosphorylation at S789 (P = 0.0859);.;.;.;
MVP
0.96
MPC
0.42
ClinPred
0.039
T
GERP RS
4.9
Varity_R
0.54
gMVP
0.65

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.12
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.

Other links and lift over

dbSNP: rs139582255; hg19: chr6-39311554; COSMIC: COSV99038495; API