chr8-29205655-T-G

Position:

• chr8-29205655-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.150-9456A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 152,008 control chromosomes in the GnomAD database, including 21,895 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 0.53 (21895 hom., cov: 31)
• Consequence: KIF13B NM_015254.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

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]

KIF13B (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF13B	NM_015254.4	c.150-9456A>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.150-9456A>C		intron_variant		1	NM_015254.4	ENSP00000427900.1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80293 AN: 151890 Hom.: 21894 Cov.: 31

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.528 AC: 80315 AN: 152008 Hom.: 21895 Cov.: 31 AF XY: 0.525 AC XY: 39007 AN XY: 74320

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.493

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.547

Alfa AF: 0.588 Hom.: 12123

Bravo AF: 0.527

Asia WGS AF: 0.421 AC: 1465 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.2
DANN	Benign	0.70

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: rs6991271; hg19: chr8-29063172;