6-39549714-G-C

Variant names:

• chr6-39549714-G-C
• rs11752175
• NM_145027.6:c.1182-4026C>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.1182-4026C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,034 control chromosomes in the GnomAD database, including 5,742 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 0.24 (5742 hom., cov: 32)
• Consequence: KIF6 NM_145027.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.417 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF6	NM_145027.6	c.1182-4026C>G		intron_variant	Intron 10 of 22	ENST00000287152.12	NP_659464.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF6	ENST00000287152.12	c.1182-4026C>G		intron_variant	Intron 10 of 22	2	NM_145027.6	ENSP00000287152.7
KIF6	ENST00000458470.5	c.855-4026C>G		intron_variant	Intron 7 of 18	1		ENSP00000409417.1
KIF6	ENST00000538893.5	c.-298-4026C>G		intron_variant	Intron 10 of 21	5		ENSP00000441435.2

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37047 AN: 151916 Hom.: 5735 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.0396

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.244 AC: 37095 AN: 152034 Hom.: 5742 Cov.: 32 AF XY: 0.247 AC XY: 18355 AN XY: 74336

African (AFR) AF: 0.422 AC: 17493 AN: 41414

American (AMR) AF: 0.272 AC: 4153 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3462

East Asian (EAS) AF: 0.0397 AC: 206 AN: 5188

South Asian (SAS) AF: 0.310 AC: 1496 AN: 4822

European-Finnish (FIN) AF: 0.130 AC: 1380 AN: 10580

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11111 AN: 67990

Other (OTH) AF: 0.229 AC: 484 AN: 2110

Alfa AF: 0.0841 Hom.: 103

Bravo AF: 0.256

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.53
PhyloP100		0.15
Mutation Taster		=97/3	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

Publications

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Other links and lift over

dbSNP: rs11752175; hg19: chr6-39517490;