dbSNP rs6728684: KIF3C:c.*1074A>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. Variant has been reported in ClinVar as (no stars).

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002254.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF3C	NM_002254.8	MANE Select	c.*1074A>C		3_prime_UTR	Exon 8 of 8	NP_002245.4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KIF3C	ENST00000264712.8	TSL:1 MANE Select	c.*1074A>C	3_prime_UTR	Exon 8 of 8	ENSP00000264712.3	O14782
KIF3C	ENST00000417737.5	TSL:1	n.*1512A>C	non_coding_transcript_exon	Exon 9 of 9	ENSP00000393676.1	F8WER6
KIF3C	ENST00000455394.5	TSL:1	n.*1561A>C	non_coding_transcript_exon	Exon 9 of 9	ENSP00000410407.1	F8WAR6

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

Age Distribution

Genome Het

Genome Hom

Variant carriers

812

1624

2436

3248

4060

<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:

0.760

Hom.:

55718

Bravo

AF:

0.692

Asia WGS

AF:

0.505

AC:

1760

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over