6-39446251-G-T

Variant names:

• chr6-39446251-G-T
• rs4236064
• NM_145027.6:c.1646-15090C>A

Variant summary

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

The NM_145027.6(KIF6):​c.1646-15090C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,054 control chromosomes in the GnomAD database, including 8,779 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 0.30 (8779 hom., cov: 32)
• Consequence: KIF6 NM_145027.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.53 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF6	NM_145027.6	c.1646-15090C>A		intron_variant	Intron 13 of 22	ENST00000287152.12	NP_659464.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF6	ENST00000287152.12	c.1646-15090C>A		intron_variant	Intron 13 of 22	2	NM_145027.6	ENSP00000287152.7
KIF6	ENST00000458470.5	c.1319-15090C>A		intron_variant	Intron 10 of 18	1		ENSP00000409417.1
KIF6	ENST00000538893.5	c.-2-15090C>A		intron_variant	Intron 12 of 21	5		ENSP00000441435.2

Frequencies

GnomAD3 genomes AF: 0.303 AC: 45966 AN: 151936 Hom.: 8745 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.303 AC: 46050 AN: 152054 Hom.: 8779 Cov.: 32 AF XY: 0.302 AC XY: 22429 AN XY: 74326

African (AFR) AF: 0.536 AC: 22196 AN: 41440

American (AMR) AF: 0.324 AC: 4953 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3472

East Asian (EAS) AF: 0.263 AC: 1362 AN: 5174

South Asian (SAS) AF: 0.159 AC: 764 AN: 4818

European-Finnish (FIN) AF: 0.201 AC: 2125 AN: 10578

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13144 AN: 67974

Other (OTH) AF: 0.314 AC: 664 AN: 2114

Alfa AF: 0.269 Hom.: 5319

Bravo AF: 0.325

Asia WGS AF: 0.242 AC: 840 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.38
PhyloP100		0.10
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: rs4236064; hg19: chr6-39414027;