rs9410888

Positions:

• chr9-83850487-G-A
• chr9-83850487-G-T

Variant summary

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

The NM_017576.4(KIF27):​c.3358-190C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 151,812 control chromosomes in the GnomAD database, including 6,909 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 0.29 (6909 hom., cov: 31)
• Consequence: KIF27 NM_017576.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

Genes affected

KIF27 (HGNC:18632): (kinesin family member 27) This gene is a member of the KIF27 (kinesin 4) sub-family of the mammalian kinesin family. The gene is an ortholog of the Drosophila Cos2 gene, which plays an important role in the Hedgehog signaling pathway. The encoded protein contains an N-terminal motor domain which includes nucleotide-binding and microtubule-interacting regions, a stalk domain containing a predicted coiled coil motif and a C-terminal tail domain. Alternatively spliced transcript variants have been observed for this gene. Pseudogenes associated with this gene are located on chromosome 9. [provided by RefSeq, Dec 2012]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF27	NM_017576.4	c.3358-190C>T		intron_variant		ENST00000297814.7	NP_060046.1
LOC124900638	XR_007061620.1	n.263+896G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF27	ENST00000297814.7	c.3358-190C>T		intron_variant		1	NM_017576.4	ENSP00000297814	P1
	ENST00000591217.5	n.582+896G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44692 AN: 151692 Hom.: 6909 Cov.: 31

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.356

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.295 AC: 44716 AN: 151812 Hom.: 6909 Cov.: 31 AF XY: 0.296 AC XY: 21961 AN XY: 74196

Gnomad4 AFR AF: 0.393

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.268

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.261

Gnomad4 OTH AF: 0.297

Alfa AF: 0.287 Hom.: 815

Bravo AF: 0.292

Asia WGS AF: 0.305 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.5
DANN	Benign	0.72

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: rs9410888; hg19: chr9-86465402;