dbSNP rs6728684: KIF3C:n.*1512A>C (chr2-25927904-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002254.8(KIF3C):c.*1074A>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 152,496 control chromosomes in the GnomAD database, including 39,541 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 0.71 ( 39452 hom., cov: 32)

Exomes 𝑓: 0.65 ( 89 hom. )

Consequence

KIF3C
NM_002254.8 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.17

Publications

16 publications found

Variant links:

Genes affected

KIF3C (HGNC:6321): (kinesin family member 3C) Predicted to enable microtubule binding activity and microtubule motor activity. Predicted to be involved in microtubule-based movement. Predicted to act upstream of or within organelle transport along microtubule. Predicted to be located in microtubule cytoskeleton; neuronal cell body; and neuronal ribonucleoprotein granule. Predicted to be part of kinesin complex. Predicted to be active in microtubule. [provided by Alliance of Genome Resources, Apr 2022]

KIF3C links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.56).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF3C	NM_002254.8 link	c.*1074A>C		3_prime_UTR_variant	Exon 8 of 8	ENST00000264712.8	NP_002245.4	O14782A2RU78
KIF3C	XM_005264299.4 link	c.*1074A>C		3_prime_UTR_variant	Exon 8 of 8		XP_005264356.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF3C	ENST00000264712.8 link	c.*1074A>C		3_prime_UTR_variant	Exon 8 of 8	1	NM_002254.8	ENSP00000264712.3		O14782

Frequencies

GnomAD3 genomes

AF:

0.707

AC:

107374

AN:

151944

Hom.:

39399

Cov.:

show subpopulations

Gnomad AFR

AF:

0.682

Gnomad AMI

AF:

0.797

Gnomad AMR

AF:

0.577

Gnomad ASJ

AF:

0.790

Gnomad EAS

AF:

0.143

Gnomad SAS

AF:

0.760

Gnomad FIN

AF:

0.636

Gnomad MID

AF:

0.741

Gnomad NFE

AF:

0.795

Gnomad OTH

AF:

0.702

GnomAD4 exome

AF:

0.650

AC:

282

AN:

434

Hom.:

Cov.:

AF XY:

0.681

AC XY:

177

AN XY:

260

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.648

AC:

276

AN:

426

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

1.00

AC:

AN:

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.512

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.707

AC:

107486

AN:

152062

Hom.:

39452

Cov.:

AF XY:

0.694

AC XY:

51615

AN XY:

74352

show subpopulations

African (AFR)

AF:

0.683

AC:

28308

AN:

41456

American (AMR)

AF:

0.577

AC:

8810

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.790

AC:

2740

AN:

3470

East Asian (EAS)

AF:

0.143

AC:

742

AN:

5182

South Asian (SAS)

AF:

0.759

AC:

3658

AN:

4818

European-Finnish (FIN)

AF:

0.636

AC:

6721

AN:

10572

Middle Eastern (MID)

AF:

0.748

AC:

220

AN:

294

European-Non Finnish (NFE)

AF:

0.795

AC:

54070

AN:

67988

Other (OTH)

AF:

0.707

AC:

1492

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1478

2956

4433

5911

7389

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.760

Hom.:

55718

Bravo

AF:

0.692

Asia WGS

AF:

0.505

AC:

1760

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.56

CADD

Benign

8.3

(source)

DANN

Benign

0.81

PhyloP100

1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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rs6728684

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over