8-29137505-A-G

Variant names:

• chr8-29137505-A-G
• rs13251954
• NM_015254.4:c.2613+2558T>C

Variant summary

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

The NM_015254.4(KIF13B):​c.2613+2558T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,166 control chromosomes in the GnomAD database, including 28,905 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 0.60 (28905 hom., cov: 33)
• Consequence: KIF13B NM_015254.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.791
• Publications: 7 publications found

Genes affected

KIF13B (HGNC:14405): (kinesin family member 13B) Enables 14-3-3 protein binding activity and protein kinase binding activity. Involved in regulation of axonogenesis. Located in axon and cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000254129 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015254.4. 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
	KIF13B	NM_015254.4	MANE Select	c.2613+2558T>C		intron	N/A	NP_056069.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF13B	ENST00000524189.6	TSL:1 MANE Select	c.2613+2558T>C		intron	N/A	ENSP00000427900.1
	ENSG00000254129	ENST00000523661.1	TSL:3	n.99-1020A>G		intron	N/A
	ENSG00000254129	ENST00000826663.1		n.489-1020A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.601 AC: 91323 AN: 152048 Hom.: 28889 Cov.: 33

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.671

Gnomad AMR AF: 0.522

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.710

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.600 AC: 91368 AN: 152166 Hom.: 28905 Cov.: 33 AF XY: 0.595 AC XY: 44294 AN XY: 74404

African (AFR) AF: 0.474 AC: 19661 AN: 41502

American (AMR) AF: 0.522 AC: 7974 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2271 AN: 3472

East Asian (EAS) AF: 0.181 AC: 935 AN: 5174

South Asian (SAS) AF: 0.568 AC: 2737 AN: 4818

European-Finnish (FIN) AF: 0.710 AC: 7525 AN: 10596

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48138 AN: 68004

Other (OTH) AF: 0.619 AC: 1307 AN: 2110

Alfa AF: 0.654 Hom.: 60805

Bravo AF: 0.579

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.21
PhyloP100		0.79
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: rs13251954; hg19: chr8-28995022;