NM_145027.6:c.1862-1214C>T

Variant names:

• chr6-39363732-G-A
• rs9394585
• NM_145027.6:c.1862-1214C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145027.6(KIF6):​c.1862-1214C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,026 control chromosomes in the GnomAD database, including 35,066 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 0.68 (35066 hom., cov: 32)
• Consequence: KIF6 NM_145027.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 5 publications found

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]

LOC107986594 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_145027.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF6	NM_145027.6	MANE Select	c.1862-1214C>T		intron	N/A	NP_659464.3
	KIF6	NM_001289020.3		c.1811-1214C>T		intron	N/A	NP_001275949.1
	KIF6	NM_001289021.3		c.1694-1214C>T		intron	N/A	NP_001275950.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF6	ENST00000287152.12	TSL:2 MANE Select	c.1862-1214C>T		intron	N/A	ENSP00000287152.7
	KIF6	ENST00000458470.5	TSL:1	c.1535-1214C>T		intron	N/A	ENSP00000409417.1
	KIF6	ENST00000229913.9	TSL:1	c.215-1214C>T		intron	N/A	ENSP00000229913.5

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102898 AN: 151908 Hom.: 35032 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.654

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.677 AC: 102977 AN: 152026 Hom.: 35066 Cov.: 32 AF XY: 0.675 AC XY: 50182 AN XY: 74300

African (AFR) AF: 0.672 AC: 27838 AN: 41444

American (AMR) AF: 0.694 AC: 10608 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2223 AN: 3466

East Asian (EAS) AF: 0.608 AC: 3141 AN: 5166

South Asian (SAS) AF: 0.493 AC: 2375 AN: 4818

European-Finnish (FIN) AF: 0.749 AC: 7921 AN: 10572

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46690 AN: 67978

Other (OTH) AF: 0.651 AC: 1365 AN: 2098

Alfa AF: 0.678 Hom.: 150928

Bravo AF: 0.675

Asia WGS AF: 0.581 AC: 2018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.093
DANN	Benign	0.14
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9394585; hg19: chr6-39331508;