chr6-39339738-T-G

Position:

• chr6-39339738-T-G

Variant summary

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

The NM_145027.6(KIF6):​c.2429-3190A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 151,966 control chromosomes in the GnomAD database, including 14,194 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 0.40 (14194 hom., cov: 33)
• Consequence: KIF6 NM_145027.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.69

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=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF6	NM_145027.6	c.2429-3190A>C		intron_variant		ENST00000287152.12	NP_659464.3
LOC105375047	XR_926774.3	n.435+1060T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF6	ENST00000287152.12	c.2429-3190A>C		intron_variant		2	NM_145027.6	ENSP00000287152	P1
KIF6	ENST00000229913.9	c.782-3190A>C		intron_variant		1		ENSP00000229913
KIF6	ENST00000458470.5	c.2053-3190A>C		intron_variant		1		ENSP00000409417
KIF6	ENST00000394362.5	c.731-3190A>C		intron_variant		5		ENSP00000377889

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61057 AN: 151848 Hom.: 14162 Cov.: 33

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.402 AC: 61145 AN: 151966 Hom.: 14194 Cov.: 33 AF XY: 0.400 AC XY: 29678 AN XY: 74260

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.469

Gnomad4 SAS AF: 0.303

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.372

Alfa AF: 0.322 Hom.: 3942

Bravo AF: 0.411

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	14
DANN	Benign	0.49

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: rs3818308; hg19: chr6-39307514;