rs9410888

Variant names:

• chr9-83850487-G-A
• rs9410888
• NM_017576.4:c.3358-190C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ENSG00000226877 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017576.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF27	NM_017576.4	MANE Select	c.3358-190C>T		intron	N/A	NP_060046.1
	KIF27	NM_001271927.3		c.3160-190C>T		intron	N/A	NP_001258856.1
	KIF27	NM_001271928.3		c.3067-190C>T		intron	N/A	NP_001258857.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF27	ENST00000297814.7	TSL:1 MANE Select	c.3358-190C>T		intron	N/A	ENSP00000297814.2
	KIF27	ENST00000413982.5	TSL:1	c.3160-190C>T		intron	N/A	ENSP00000401688.1
	KIF27	ENST00000334204.6	TSL:1	c.3067-190C>T		intron	N/A	ENSP00000333928.2

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

African (AFR) AF: 0.393 AC: 16251 AN: 41354

American (AMR) AF: 0.208 AC: 3170 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3468

East Asian (EAS) AF: 0.266 AC: 1365 AN: 5132

South Asian (SAS) AF: 0.370 AC: 1782 AN: 4814

European-Finnish (FIN) AF: 0.248 AC: 2625 AN: 10568

Middle Eastern (MID) AF: 0.345 AC: 100 AN: 290

European-Non Finnish (NFE) AF: 0.261 AC: 17734 AN: 67910

Other (OTH) AF: 0.297 AC: 624 AN: 2100

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.5
DANN	Benign	0.72
PhyloP100		0.035
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: rs9410888; hg19: chr9-86465402;