6-39561206-G-A

Variant names:

• chr6-39561206-G-A
• rs9380880
• NM_145027.6:c.1182-15518C>T

Variant summary

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

The NM_145027.6(KIF6):​c.1182-15518C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.04 in 152,272 control chromosomes in the GnomAD database, including 274 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 0.040 (274 hom., cov: 33)
• Consequence: KIF6 NM_145027.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.647
• Publications: 5 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF6	NM_145027.6	c.1182-15518C>T		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.1182-15518C>T		intron_variant	Intron 10 of 22	2	NM_145027.6	ENSP00000287152.7
KIF6	ENST00000458470.5	c.855-15518C>T		intron_variant	Intron 7 of 18	1		ENSP00000409417.1
KIF6	ENST00000538893.5	c.-298-15518C>T		intron_variant	Intron 10 of 21	5		ENSP00000441435.2

Frequencies

GnomAD3 genomes AF: 0.0400 AC: 6090 AN: 152152 Hom.: 275 Cov.: 33

Gnomad AFR AF: 0.0304

Gnomad AMI AF: 0.0395

Gnomad AMR AF: 0.0228

Gnomad ASJ AF: 0.0383

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.0329

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0406

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

GnomAD4 genome AF: 0.0400 AC: 6087 AN: 152272 Hom.: 274 Cov.: 33 AF XY: 0.0427 AC XY: 3180 AN XY: 74436

African (AFR) AF: 0.0303 AC: 1258 AN: 41568

American (AMR) AF: 0.0230 AC: 352 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.0383 AC: 133 AN: 3470

East Asian (EAS) AF: 0.253 AC: 1308 AN: 5168

South Asian (SAS) AF: 0.0941 AC: 454 AN: 4824

European-Finnish (FIN) AF: 0.0329 AC: 349 AN: 10592

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0309 AC: 2100 AN: 68020

Other (OTH) AF: 0.0411 AC: 87 AN: 2116

Alfa AF: 0.0383 Hom.: 736

Bravo AF: 0.0393

Asia WGS AF: 0.149 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.20
PhyloP100		0.65
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: rs9380880; hg19: chr6-39528982;