chr8-29200391-G-A

Variant names:

• chr8-29200391-G-A
• rs17456025
• NM_015254.4:c.150-4192C>T

Variant summary

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

The NM_015254.4(KIF13B):​c.150-4192C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,142 control chromosomes in the GnomAD database, including 1,242 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 0.12 (1242 hom., cov: 32)
• Consequence: KIF13B NM_015254.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.138 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF13B	NM_015254.4	c.150-4192C>T		intron_variant	Intron 2 of 39	ENST00000524189.6	NP_056069.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF13B	ENST00000524189.6	c.150-4192C>T		intron_variant	Intron 2 of 39	1	NM_015254.4	ENSP00000427900.1

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18185 AN: 152024 Hom.: 1233 Cov.: 32

Gnomad AFR AF: 0.0901

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0935

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.0202

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.120 AC: 18217 AN: 152142 Hom.: 1242 Cov.: 32 AF XY: 0.121 AC XY: 9004 AN XY: 74354

African (AFR) AF: 0.0901 AC: 3741 AN: 41506

American (AMR) AF: 0.0934 AC: 1428 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 612 AN: 3470

East Asian (EAS) AF: 0.0202 AC: 105 AN: 5186

South Asian (SAS) AF: 0.147 AC: 709 AN: 4820

European-Finnish (FIN) AF: 0.198 AC: 2091 AN: 10548

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9171 AN: 68008

Other (OTH) AF: 0.126 AC: 267 AN: 2114

Alfa AF: 0.128 Hom.: 664

Bravo AF: 0.110

Asia WGS AF: 0.107 AC: 370 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	4.0
DANN	Benign	0.17
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

Publications

LitVar

Other links and lift over

dbSNP: rs17456025; hg19: chr8-29057908;