rs12682543

Positions:

• chr8-29222041-G-A
• chr8-29222041-G-C

Variant summary

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

The NM_015254.4(KIF13B):​c.149+23305C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,764 control chromosomes in the GnomAD database, including 24,724 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 0.54 (24724 hom., cov: 31)
• Consequence: KIF13B NM_015254.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820

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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.673 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF13B	NM_015254.4	c.149+23305C>T		intron_variant		ENST00000524189.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF13B	ENST00000524189.6	c.149+23305C>T		intron_variant		1	NM_015254.4	P1

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82647 AN: 151650 Hom.: 24723 Cov.: 31

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.587

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.545 AC: 82667 AN: 151764 Hom.: 24724 Cov.: 31 AF XY: 0.541 AC XY: 40123 AN XY: 74144

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.594

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.578

Alfa AF: 0.650 Hom.: 33884

Bravo AF: 0.533

Asia WGS AF: 0.434 AC: 1509 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.59

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: rs12682543; hg19: chr8-29079558;