rs9394587

Positions:

• chr6-39381025-C-A
• chr6-39381025-C-G

Variant summary

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

The NM_145027.6(KIF6):​c.1861+4597G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 152,070 control chromosomes in the GnomAD database, including 14,440 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 0.41 (14440 hom., cov: 32)
• Consequence: KIF6 NM_145027.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF6	NM_145027.6	c.1861+4597G>T		intron_variant		ENST00000287152.12
LOC107986594	XR_001744111.2	n.401-7284C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF6	ENST00000287152.12	c.1861+4597G>T		intron_variant		2	NM_145027.6	P1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61790 AN: 151952 Hom.: 14438 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.406 AC: 61790 AN: 152070 Hom.: 14440 Cov.: 32 AF XY: 0.410 AC XY: 30439 AN XY: 74330

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.522

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.343

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.402

Alfa AF: 0.472 Hom.: 22870

Bravo AF: 0.395

Asia WGS AF: 0.426 AC: 1477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.89
DANN	Benign	0.73

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: rs9394587; hg19: chr6-39348801;