Variant 6-33409703-ATC-ATCTC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000428849.7(KIFC1):c.*15_*16dup variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0232 in 1,320,974 control chromosomes in the GnomAD database, including 2,522 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.061 ( 255 hom., cov: 28)

Exomes 𝑓: 0.021 ( 2267 hom. )

Consequence

KIFC1
ENST00000428849.7 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.491

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 Benign. Variant got -10 ACMG points.

BP6

Variant 6-33409703-A-ATC is Benign according to our data. Variant chr6-33409703-A-ATC is described in ClinVar as [Benign]. Clinvar id is 403017.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE	Protein
KIFC1	NM_002263.4 linkuse as main transcript	c.15_16dup	3_prime_UTR_variant	11/11	ENST00000428849.7	NP_002254.2
KIFC1	XM_011514585.2 linkuse as main transcript	c.100_101dup	3_prime_UTR_variant	12/12		XP_011512887.1
KIFC1	XM_011514587.3 linkuse as main transcript	c.15_16dup	3_prime_UTR_variant	10/10		XP_011512889.1
KIFC1	XM_017010837.2 linkuse as main transcript	c.15_16dup	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_16dup		3_prime_UTR_variant	11/11	1	NM_002263.4	ENSP00000393963	P1

Frequencies

GnomAD3 genomes

AF:

0.0610

AC:

5297

AN:

86778

Hom.:

255

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0497

Gnomad AMI

AF:

0.00147

Gnomad AMR

AF:

0.0745

Gnomad ASJ

AF:

0.0592

Gnomad EAS

AF:

0.0792

Gnomad SAS

AF:

0.0594

Gnomad FIN

AF:

0.0968

Gnomad MID

AF:

0.0455

Gnomad NFE

AF:

0.0614

Gnomad OTH

AF:

0.0593

GnomAD3 exomes

AF:

0.0250

AC:

4808

AN:

192512

Hom.:

333

AF XY:

0.0252

AC XY:

2644

AN XY:

104726

show subpopulations

Gnomad AFR exome

AF:

0.0121

Gnomad AMR exome

AF:

0.0356

Gnomad ASJ exome

AF:

0.0157

Gnomad EAS exome

AF:

0.0299

Gnomad SAS exome

AF:

0.0240

Gnomad FIN exome

AF:

0.0387

Gnomad NFE exome

AF:

0.0223

Gnomad OTH exome

AF:

0.0274

GnomAD4 exome

AF:

0.0205

AC:

25339

AN:

1234106

Hom.:

2267

Cov.:

AF XY:

0.0211

AC XY:

13017

AN XY:

617934

show subpopulations

Gnomad4 AFR exome

AF:

0.0116

Gnomad4 AMR exome

AF:

0.0344

Gnomad4 ASJ exome

AF:

0.0202

Gnomad4 EAS exome

AF:

0.0388

Gnomad4 SAS exome

AF:

0.0230

Gnomad4 FIN exome

AF:

0.0422

Gnomad4 NFE exome

AF:

0.0184

Gnomad4 OTH exome

AF:

0.0227

GnomAD4 genome

AF:

0.0610

AC:

5301

AN:

86868

Hom.:

255

Cov.:

AF XY:

0.0623

AC XY:

2569

AN XY:

41238

show subpopulations

Gnomad4 AFR

AF:

0.0498

Gnomad4 AMR

AF:

0.0743

Gnomad4 ASJ

AF:

0.0592

Gnomad4 EAS

AF:

0.0789

Gnomad4 SAS

AF:

0.0590

Gnomad4 FIN

AF:

0.0968

Gnomad4 NFE

AF:

0.0614

Gnomad4 OTH

AF:

0.0591

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Mar 28, 2016

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over