rs9471075

Variant names:

• chr6-39339256-A-C
• rs9471075
• NM_145027.6:c.2429-2708T>G

Variant summary

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

The NM_145027.6(KIF6):​c.2429-2708T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,106 control chromosomes in the GnomAD database, including 3,409 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 0.13 (3409 hom., cov: 32)
• Consequence: KIF6 NM_145027.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

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]

LOC105375047 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF6	NM_145027.6	c.2429-2708T>G		intron_variant	Intron 22 of 22	ENST00000287152.12	NP_659464.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF6	ENST00000287152.12	c.2429-2708T>G		intron_variant	Intron 22 of 22	2	NM_145027.6	ENSP00000287152.7
KIF6	ENST00000458470.5	c.2051-2708T>G		intron_variant	Intron 18 of 18	1		ENSP00000409417.1
KIF6	ENST00000229913.9	c.782-2708T>G		intron_variant	Intron 9 of 9	1		ENSP00000229913.5
KIF6	ENST00000394362.5	c.731-2708T>G		intron_variant	Intron 8 of 8	5		ENSP00000377889.1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20190 AN: 151986 Hom.: 3391 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0693

Gnomad ASJ AF: 0.0482

Gnomad EAS AF: 0.00193

Gnomad SAS AF: 0.00848

Gnomad FIN AF: 0.0350

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0285

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.133 AC: 20253 AN: 152106 Hom.: 3409 Cov.: 32 AF XY: 0.129 AC XY: 9626 AN XY: 74362

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.0692

Gnomad4 ASJ AF: 0.0482

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.00828

Gnomad4 FIN AF: 0.0350

Gnomad4 NFE AF: 0.0285

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0554 Hom.: 401

Bravo AF: 0.150

Asia WGS AF: 0.0310 AC: 109 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	0.18
DANN	Benign	0.52

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: rs9471075; hg19: chr6-39307032;