2-25933786-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF3C	NM_002254.8	c.2007-3723G>A		intron_variant	Intron 5 of 7	ENST00000264712.8	NP_002245.4
KIF3C	XM_005264299.4	c.2007-3726G>A		intron_variant	Intron 5 of 7		XP_005264356.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF3C	ENST00000264712.8	c.2007-3723G>A		intron_variant	Intron 5 of 7	1	NM_002254.8	ENSP00000264712.3

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

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.0954

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.561

Alfa AF: 0.685 Hom.: 26955

Bravo AF: 0.520

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.19

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

LitVar

Other links and lift over

dbSNP: rs2384298; hg19: chr2-26156655;