6-39365561-T-C

Variant names:

• chr6-39365561-T-C
• rs9357303
• NM_145027.6:c.1862-3043A>G

Variant summary

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

The NM_145027.6(KIF6):​c.1862-3043A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 152,164 control chromosomes in the GnomAD database, including 11,739 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 0.36 (11739 hom., cov: 33)
• Consequence: KIF6 NM_145027.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.93
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF6	NM_145027.6	c.1862-3043A>G		intron_variant	Intron 16 of 22	ENST00000287152.12	NP_659464.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF6	ENST00000287152.12	c.1862-3043A>G		intron_variant	Intron 16 of 22	2	NM_145027.6	ENSP00000287152.7

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55121 AN: 152046 Hom.: 11737 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.459

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.362 AC: 55127 AN: 152164 Hom.: 11739 Cov.: 33 AF XY: 0.365 AC XY: 27161 AN XY: 74392

African (AFR) AF: 0.125 AC: 5183 AN: 41534

American (AMR) AF: 0.459 AC: 7022 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1573 AN: 3470

East Asian (EAS) AF: 0.381 AC: 1971 AN: 5176

South Asian (SAS) AF: 0.278 AC: 1341 AN: 4818

European-Finnish (FIN) AF: 0.536 AC: 5664 AN: 10570

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31212 AN: 67994

Other (OTH) AF: 0.348 AC: 734 AN: 2110

Alfa AF: 0.425 Hom.: 23533

Bravo AF: 0.347

Asia WGS AF: 0.316 AC: 1099 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.067
DANN	Benign	0.28
PhyloP100		-3.9
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: rs9357303; hg19: chr6-39333337;