6-168012515-C-T

Variant names:

• chr6-168012515-C-T
• rs1858675
• NM_030615.4:c.-162-5458C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_030615.4(KIF25):​c.-162-5458C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,962 control chromosomes in the GnomAD database, including 9,039 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 0.34 (9039 hom., cov: 33)
• Consequence: KIF25 NM_030615.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 12 publications found

Genes affected

KIF25 (HGNC:6390): (kinesin family member 25) The protein encoded by this gene is a member of the kinesin-like protein family. Protein family members are microtubule-dependent molecular motors that transport organelles within cells and move chromosomes during cell division. However, the particular function of this gene product has not yet been determined. Two alternatively spliced transcript variants which encode products have been described. Other splice variants have been found that lack exon 2 and the initiation codon for translation. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030615.4. 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
	KIF25	NM_030615.4	MANE Select	c.-162-5458C>T		intron	N/A	NP_085118.2
	KIF25	NM_005355.5		c.-162-5458C>T		intron	N/A	NP_005346.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF25	ENST00000643607.3	MANE Select	c.-162-5458C>T		intron	N/A	ENSP00000496229.1
	KIF25	ENST00000443060.6	TSL:5	c.-162-5458C>T		intron	N/A	ENSP00000388878.2
	KIF25	ENST00000652547.1		c.-162-5458C>T		intron	N/A	ENSP00000498669.1

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51329 AN: 151844 Hom.: 9019 Cov.: 33

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.338 AC: 51389 AN: 151962 Hom.: 9039 Cov.: 33 AF XY: 0.347 AC XY: 25743 AN XY: 74268

African (AFR) AF: 0.221 AC: 9142 AN: 41442

American (AMR) AF: 0.335 AC: 5108 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1332 AN: 3464

East Asian (EAS) AF: 0.390 AC: 2013 AN: 5166

South Asian (SAS) AF: 0.425 AC: 2041 AN: 4808

European-Finnish (FIN) AF: 0.501 AC: 5293 AN: 10556

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25176 AN: 67942

Other (OTH) AF: 0.335 AC: 708 AN: 2114

Alfa AF: 0.350 Hom.: 31317

Bravo AF: 0.318

Asia WGS AF: 0.413 AC: 1432 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.65
PhyloP100		0.19
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: rs1858675; hg19: chr6-168413195;