Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_002263.4(KIFC1):c.*15_*16dupCT 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
NM_002263.4 3_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.491

Publications

0 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002263.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIFC1	NM_002263.4	MANE Select	c.15_16dupCT		3_prime_UTR	Exon 11 of 11	NP_002254.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIFC1	ENST00000428849.7	TSL:1 MANE Select	c.15_16dupCT		3_prime_UTR	Exon 11 of 11	ENSP00000393963.2

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

GnomAD2 exomes

AF:

0.0250

AC:

4808

AN:

192512

AF XY:

0.0252

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 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

African (AFR)

AF:

0.0116

AC:

347

AN:

29982

American (AMR)

AF:

0.0344

AC:

1344

AN:

39066

Ashkenazi Jewish (ASJ)

AF:

0.0202

AC:

448

AN:

22146

East Asian (EAS)

AF:

0.0388

AC:

1281

AN:

33020

South Asian (SAS)

AF:

0.0230

AC:

1792

AN:

77876

European-Finnish (FIN)

AF:

0.0422

AC:

1580

AN:

37414

Middle Eastern (MID)

AF:

0.0177

AC:

AN:

3958

European-Non Finnish (NFE)

AF:

0.0184

AC:

17325

AN:

939880

Other (OTH)

AF:

0.0227

AC:

1152

AN:

50764

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.401

Heterozygous variant carriers

657

1314

1970

2627

3284

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

400

800

1200

1600

2000

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0610

AC:

5301

AN:

86868

Hom.:

255

Cov.:

AF XY:

0.0623

AC XY:

2569

AN XY:

41238

show subpopulations

African (AFR)

AF:

0.0498

AC:

1188

AN:

23862

American (AMR)

AF:

0.0743

AC:

588

AN:

7914

Ashkenazi Jewish (ASJ)

AF:

0.0592

AC:

118

AN:

1992

East Asian (EAS)

AF:

0.0789

AC:

214

AN:

2714

South Asian (SAS)

AF:

0.0590

AC:

130

AN:

2204

European-Finnish (FIN)

AF:

0.0968

AC:

409

AN:

4226

Middle Eastern (MID)

AF:

0.0488

AC:

AN:

164

European-Non Finnish (NFE)

AF:

0.0614

AC:

2578

AN:

41976

Other (OTH)

AF:

0.0591

AC:

AN:

1134

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

221

442

664

885

1106

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

180

240

300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0882

Hom.:

430

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.49

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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6-33409703-ATC-ATCTC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

ClinVar submissions as Germline

Computational scores

Splicing

Publications

Other links and lift over