NM_030615.4:c.-162-667C>A

Variant names:

• chr6-168017306-C-A
• rs3807061
• NM_030615.4:c.-162-667C>A

Variant summary

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

The NM_030615.4(KIF25):​c.-162-667C>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
• Publications: 8 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=-0.87).
• 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 rank	MANE	Protein	UniProt
KIF25	NM_030615.4	c.-162-667C>A		intron_variant	Intron 4 of 12	ENST00000643607.3	NP_085118.2
KIF25	NM_005355.5	c.-162-667C>A		intron_variant	Intron 4 of 11		NP_005346.3
KIF25	XM_047418749.1	c.-162-667C>A		intron_variant	Intron 2 of 10		XP_047274705.1
KIF25	XM_011535803.4	c.-162-667C>A		intron_variant	Intron 2 of 9		XP_011534105.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF25	ENST00000643607.3	c.-162-667C>A		intron_variant	Intron 4 of 12		NM_030615.4	ENSP00000496229.1
KIF25	ENST00000443060.6	c.-162-667C>A		intron_variant	Intron 1 of 9	5		ENSP00000388878.2
KIF25	ENST00000652547.1	c.-162-667C>A		intron_variant	Intron 1 of 5			ENSP00000498669.1
KIF25	ENST00000515361.5	n.415-667C>A		intron_variant	Intron 4 of 5	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

African (AFR) AF: 0.269 AC: 11144 AN: 41482

American (AMR) AF: 0.357 AC: 5461 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1468 AN: 3464

East Asian (EAS) AF: 0.416 AC: 2147 AN: 5158

South Asian (SAS) AF: 0.425 AC: 2049 AN: 4816

European-Finnish (FIN) AF: 0.517 AC: 5463 AN: 10568

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27133 AN: 67936

Other (OTH) AF: 0.361 AC: 762 AN: 2112

Alfa AF: 0.378 Hom.: 14311

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
PhyloP100		-1.0
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: rs3807061; hg19: chr6-168417986; COSMIC: COSV63026928; COSMIC: COSV63026928;