2-25933786-C-T

Variant names:

• chr2-25933786-C-T
• rs2384298
• NM_002254.8:c.2007-3723G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002254.8(KIF3C):​c.2007-3723G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.55 in 151,654 control chromosomes in the GnomAD database, including 26,145 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 0.55 (26145 hom., cov: 31)
• Consequence: KIF3C NM_002254.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.513
• Publications: 6 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.728 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.2007-3723G>A		intron	N/A	NP_002245.4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF3C	ENST00000264712.8	TSL:1 MANE Select	c.2007-3723G>A		intron	N/A	ENSP00000264712.3	O14782
	KIF3C	ENST00000417737.5	TSL:1	n.*63-3723G>A		intron	N/A	ENSP00000393676.1	F8WER6
	KIF3C	ENST00000455394.5	TSL:1	n.*111+247G>A		intron	N/A	ENSP00000410407.1	F8WAR6

Frequencies

GnomAD3 genomes AF: 0.550 AC: 83352 AN: 151544 Hom.: 26129 Cov.: 31

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.0950

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.555

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.550 AC: 83399 AN: 151654 Hom.: 26145 Cov.: 31 AF XY: 0.540 AC XY: 40003 AN XY: 74094

African (AFR) AF: 0.298 AC: 12315 AN: 41282

American (AMR) AF: 0.480 AC: 7300 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.675 AC: 2342 AN: 3468

East Asian (EAS) AF: 0.0954 AC: 492 AN: 5158

South Asian (SAS) AF: 0.575 AC: 2765 AN: 4808

European-Finnish (FIN) AF: 0.616 AC: 6451 AN: 10480

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49849 AN: 67952

Other (OTH) AF: 0.561 AC: 1180 AN: 2102

Alfa AF: 0.679 Hom.: 31212

Bravo AF: 0.520

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.19
PhyloP100		0.51
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2384298; hg19: chr2-26156655;