Variant rs752059822 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The ENST00000428849.7(KIFC1):c.*15_*16del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000976 in 1,332,554 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000092 ( 0 hom., cov: 15)

Exomes 𝑓: 0.0000040 ( 0 hom. )

Consequence

KIFC1
ENST00000428849.7 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.293

Variant links:

Genes affected

KIFC1 (HGNC:6389): (kinesin family member C1) Predicted to enable microtubule binding activity and minus-end-directed microtubule motor activity. Involved in mitotic metaphase plate congression and mitotic spindle assembly. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

KIFC1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High AC in GnomAd4 at 8 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
KIFC1	NM_002263.4 linkuse as main transcript	c.15_16del	3_prime_UTR_variant	11/11	ENST00000428849.7	NP_002254.2
KIFC1	XM_011514585.2 linkuse as main transcript	c.100_101del	3_prime_UTR_variant	12/12		XP_011512887.1
KIFC1	XM_011514587.3 linkuse as main transcript	c.15_16del	3_prime_UTR_variant	10/10		XP_011512889.1
KIFC1	XM_017010837.2 linkuse as main transcript	c.15_16del	3_prime_UTR_variant	11/11		XP_016866326.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIFC1	ENST00000428849.7 linkuse as main transcript	c.15_16del		3_prime_UTR_variant	11/11	1	NM_002263.4	ENSP00000393963	P1

Frequencies

GnomAD3 genomes

AF:

0.0000921

AC:

AN:

86878

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000336

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000401

AC:

AN:

1245676

Hom.:

AF XY:

0.00000481

AC XY:

AN XY:

624224

show subpopulations

Gnomad4 AFR exome

AF:

0.0000662

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000211

Gnomad4 OTH exome

AF:

0.0000195

GnomAD4 genome

AF:

0.0000921

AC:

AN:

86878

Hom.:

Cov.:

AF XY:

0.0000728

AC XY:

AN XY:

41206

show subpopulations

Gnomad4 AFR

AF:

0.000336

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over