rs9296295

Variant names:

• chr6-39394078-C-A
• rs9296295
• NM_145027.6:c.1811-8406G>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.1811-8406G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 151,980 control chromosomes in the GnomAD database, including 1,636 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 0.13 (1636 hom., cov: 32)
• Consequence: KIF6 NM_145027.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 10 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 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.1811-8406G>T		intron	N/A	NP_659464.3
	KIF6	NM_001289020.3		c.1810+25870G>T		intron	N/A	NP_001275949.1
	KIF6	NM_001289021.3		c.1643-8406G>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.1811-8406G>T		intron	N/A	ENSP00000287152.7
	KIF6	ENST00000458470.5	TSL:1	c.1484-8406G>T		intron	N/A	ENSP00000409417.1
	KIF6	ENST00000229913.9	TSL:1	c.164-8406G>T		intron	N/A	ENSP00000229913.5

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19159 AN: 151862 Hom.: 1629 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.0770

Gnomad ASJ AF: 0.0574

Gnomad EAS AF: 0.00888

Gnomad SAS AF: 0.0449

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0918

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.126 AC: 19198 AN: 151980 Hom.: 1636 Cov.: 32 AF XY: 0.125 AC XY: 9320 AN XY: 74302

African (AFR) AF: 0.225 AC: 9325 AN: 41390

American (AMR) AF: 0.0769 AC: 1174 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0574 AC: 199 AN: 3468

East Asian (EAS) AF: 0.00890 AC: 46 AN: 5168

South Asian (SAS) AF: 0.0454 AC: 219 AN: 4826

European-Finnish (FIN) AF: 0.143 AC: 1512 AN: 10564

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0918 AC: 6243 AN: 67988

Other (OTH) AF: 0.113 AC: 238 AN: 2100

Alfa AF: 0.0999 Hom.: 2933

Bravo AF: 0.127

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.023
DANN	Benign	0.30
PhyloP100		-1.0
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: rs9296295; hg19: chr6-39361854;