rs721755

Positions:

• chr6-39381754-G-A
• chr6-39381754-G-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_145027.6(KIF6):​c.1861+3868C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 152,132 control chromosomes in the GnomAD database, including 51,152 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 0.81 (51152 hom., cov: 32)
• Consequence: KIF6 NM_145027.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

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]

LOC107986594 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF6	NM_145027.6	c.1861+3868C>T		intron_variant		ENST00000287152.12	NP_659464.3
LOC107986594	XR_001744111.2	n.401-6555G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF6	ENST00000287152.12	c.1861+3868C>T		intron_variant		2	NM_145027.6	ENSP00000287152	P1

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123821 AN: 152014 Hom.: 51094 Cov.: 32

Gnomad AFR AF: 0.959

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.661

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.757

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.815 AC: 123932 AN: 152132 Hom.: 51152 Cov.: 32 AF XY: 0.813 AC XY: 60439 AN XY: 74380

Gnomad4 AFR AF: 0.959

Gnomad4 AMR AF: 0.802

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.661

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.757

Gnomad4 OTH AF: 0.787

Alfa AF: 0.760 Hom.: 57159

Bravo AF: 0.820

Asia WGS AF: 0.746 AC: 2591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
CADD	Benign	16
DANN	Benign	0.79

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: rs721755; hg19: chr6-39349530;