Genetic Variant KIF6:c.1946+30G>A (chr6-39362404-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_145027.6(KIF6):c.1946+30G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 1,565,426 control chromosomes in the GnomAD database, including 15,915 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.17 ( 2564 hom., cov: 32)

Exomes 𝑓: 0.13 ( 13351 hom. )

Consequence

KIF6
NM_145027.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.301

Publications

5 publications found

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]

KIF6 links:

LOC107986594 (HGNC:):

LOC107986594 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF6	NM_145027.6 link	c.1946+30G>A		intron_variant	Intron 17 of 22	ENST00000287152.12	NP_659464.3	Q6ZMV9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF6	ENST00000287152.12 link	c.1946+30G>A		intron_variant	Intron 17 of 22	2	NM_145027.6	ENSP00000287152.7		Q6ZMV9-1

Frequencies

GnomAD3 genomes

AF:

0.170

AC:

25750

AN:

151780

Hom.:

2563

Cov.:

show subpopulations

Gnomad AFR

AF:

0.278

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.125

Gnomad EAS

AF:

0.0490

Gnomad SAS

AF:

0.117

Gnomad FIN

AF:

0.113

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.134

Gnomad OTH

AF:

0.183

GnomAD2 exomes

AF:

0.131

AC:

32822

AN:

251198

AF XY:

0.128

show subpopulations

Gnomad AFR exome

AF:

0.285

Gnomad AMR exome

AF:

0.106

Gnomad ASJ exome

AF:

0.125

Gnomad EAS exome

AF:

0.0461

Gnomad FIN exome

AF:

0.115

Gnomad NFE exome

AF:

0.137

Gnomad OTH exome

AF:

0.147

GnomAD4 exome

AF:

0.133

AC:

187981

AN:

1413528

Hom.:

13351

Cov.:

AF XY:

0.132

AC XY:

93472

AN XY:

706024

show subpopulations

African (AFR)

AF:

0.291

AC:

9443

AN:

32468

American (AMR)

AF:

0.110

AC:

4921

AN:

44676

Ashkenazi Jewish (ASJ)

AF:

0.123

AC:

3179

AN:

25870

East Asian (EAS)

AF:

0.0436

AC:

1721

AN:

39464

South Asian (SAS)

AF:

0.110

AC:

9377

AN:

85260

European-Finnish (FIN)

AF:

0.112

AC:

5963

AN:

53392

Middle Eastern (MID)

AF:

0.180

AC:

910

AN:

5048

European-Non Finnish (NFE)

AF:

0.135

AC:

143993

AN:

1068706

Other (OTH)

AF:

0.144

AC:

8474

AN:

58644

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

8096

16191

24287

32382

40478

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5120

10240

15360

20480

25600

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.170

AC:

25775

AN:

151898

Hom.:

2564

Cov.:

AF XY:

0.167

AC XY:

12419

AN XY:

74198

show subpopulations

African (AFR)

AF:

0.277

AC:

11484

AN:

41406

American (AMR)

AF:

0.142

AC:

2171

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.125

AC:

433

AN:

3464

East Asian (EAS)

AF:

0.0491

AC:

252

AN:

5134

South Asian (SAS)

AF:

0.117

AC:

563

AN:

4794

European-Finnish (FIN)

AF:

0.113

AC:

1197

AN:

10570

Middle Eastern (MID)

AF:

0.238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.134

AC:

9137

AN:

67944

Other (OTH)

AF:

0.184

AC:

388

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1037

2074

3110

4147

5184

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

272

544

816

1088

1360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.164

Hom.:

899

Bravo

AF:

0.176

Asia WGS

AF:

0.133

AC:

464

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.68

PhyloP100

0.30

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over