rs9364385

Positions:

• chr6-168014692-G-A
• chr6-168014692-G-T

Variant summary

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

The NM_030615.4(KIF25):​c.-162-3281G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,052 control chromosomes in the GnomAD database, including 9,347 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 0.35 (9347 hom., cov: 34)
• Consequence: KIF25 NM_030615.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.438

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF25	NM_030615.4	c.-162-3281G>A		intron_variant		ENST00000643607.3
KIF25	NM_005355.5	c.-162-3281G>A		intron_variant
KIF25	XM_011535803.4	c.-162-3281G>A		intron_variant
KIF25	XM_047418749.1	c.-162-3281G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF25	ENST00000643607.3	c.-162-3281G>A		intron_variant			NM_030615.4	P1
KIF25	ENST00000443060.6	c.-162-3281G>A		intron_variant		5		P1
KIF25	ENST00000652547.1	c.-162-3281G>A		intron_variant
KIF25	ENST00000515361.5	n.415-3281G>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52673 AN: 151934 Hom.: 9324 Cov.: 34

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.337

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.388

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.347 AC: 52742 AN: 152052 Hom.: 9347 Cov.: 34 AF XY: 0.354 AC XY: 26344 AN XY: 74318

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.384

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.500

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.340

Alfa AF: 0.360 Hom.: 12805

Bravo AF: 0.328

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.58

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: rs9364385; hg19: chr6-168415372; COSMIC: COSV63026917; COSMIC: COSV63026917;