rs1885615

Positions:

• chr6-39370659-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_145027.6(KIF6):​c.1862-8141T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 152,036 control chromosomes in the GnomAD database, including 26,571 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 0.58 (26571 hom., cov: 32)
• Consequence: KIF6 NM_145027.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF6	NM_145027.6	c.1862-8141T>C		intron_variant		ENST00000287152.12	NP_659464.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF6	ENST00000287152.12	c.1862-8141T>C		intron_variant		2	NM_145027.6	ENSP00000287152.7

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88385 AN: 151918 Hom.: 26557 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.582 AC: 88437 AN: 152036 Hom.: 26571 Cov.: 32 AF XY: 0.582 AC XY: 43229 AN XY: 74320

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.596

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.477

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.570

Alfa AF: 0.622 Hom.: 5020

Bravo AF: 0.565

Asia WGS AF: 0.463 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	9.1
DANN	Benign	0.65

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: rs1885615; hg19: chr6-39338435;