8-29097375-T-G

Position:

• chr8-29097375-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015254.4(KIF13B):​c.4324+1758A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,180 control chromosomes in the GnomAD database, including 58,044 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 0.87 (58044 hom., cov: 31)
• Consequence: KIF13B NM_015254.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF13B	NM_015254.4	c.4324+1758A>C		intron_variant		ENST00000524189.6	NP_056069.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF13B	ENST00000524189.6	c.4324+1758A>C		intron_variant		1	NM_015254.4	ENSP00000427900.1
KIF13B	ENST00000523130.1	c.163+1758A>C		intron_variant		5		ENSP00000429106.1

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132141 AN: 152062 Hom.: 58003 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.869 AC: 132243 AN: 152180 Hom.: 58044 Cov.: 31 AF XY: 0.866 AC XY: 64398 AN XY: 74400

Gnomad4 AFR AF: 0.791

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.920

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.933

Gnomad4 OTH AF: 0.880

Alfa AF: 0.920 Hom.: 90425

Bravo AF: 0.860

Asia WGS AF: 0.714 AC: 2484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.47
DANN	Benign	0.39

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: rs7844537; hg19: chr8-28954892;