rs9296295

Positions:

• chr6-39394078-C-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF6	NM_145027.6	c.1811-8406G>T		intron_variant		ENST00000287152.12	NP_659464.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF6	ENST00000287152.12	c.1811-8406G>T		intron_variant		2	NM_145027.6	ENSP00000287152	P1

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

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.0769

Gnomad4 ASJ AF: 0.0574

Gnomad4 EAS AF: 0.00890

Gnomad4 SAS AF: 0.0454

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.0918

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0925 Hom.: 1016

Bravo AF: 0.127

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.023
DANN	Benign	0.30

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

Other links and lift over

dbSNP: rs9296295; hg19: chr6-39361854;