6-168017306-C-A

Position:

• chr6-168017306-C-A

Variant summary

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

The NM_030615.4(KIF25):​c.-162-667C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,018 control chromosomes in the GnomAD database, including 10,643 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 0.37 (10643 hom., cov: 33)
• Consequence: KIF25 NM_030615.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF25	NM_030615.4	c.-162-667C>A		intron_variant		ENST00000643607.3
KIF25	NM_005355.5	c.-162-667C>A		intron_variant
KIF25	XM_011535803.4	c.-162-667C>A		intron_variant
KIF25	XM_047418749.1	c.-162-667C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF25	ENST00000643607.3	c.-162-667C>A		intron_variant			NM_030615.4	P1
KIF25	ENST00000443060.6	c.-162-667C>A		intron_variant		5		P1
KIF25	ENST00000652547.1	c.-162-667C>A		intron_variant
KIF25	ENST00000515361.5	n.415-667C>A		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56131 AN: 151900 Hom.: 10621 Cov.: 33

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.424

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.370 AC: 56204 AN: 152018 Hom.: 10643 Cov.: 33 AF XY: 0.377 AC XY: 28011 AN XY: 74306

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.357

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.517

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.361

Alfa AF: 0.384 Hom.: 11279

Bravo AF: 0.352

Asia WGS AF: 0.433 AC: 1502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.41
DANN	Benign	0.78

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: rs3807061; hg19: chr6-168417986; COSMIC: COSV63026928; COSMIC: COSV63026928;