rs12056328

Positions:

• chr8-29179944-C-T

Variant summary

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

The NM_015254.4(KIF13B):​c.720+160G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,036 control chromosomes in the GnomAD database, including 21,354 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 0.51 (21354 hom., cov: 32)
• Consequence: KIF13B NM_015254.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44

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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF13B	NM_015254.4	c.720+160G>A		intron_variant		ENST00000524189.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF13B	ENST00000524189.6	c.720+160G>A		intron_variant		1	NM_015254.4	P1
KIF13B	ENST00000521515.1	c.720+160G>A		intron_variant		5
KIF13B	ENST00000522355.5	c.*367+160G>A		intron_variant, NMD_transcript_variant		2
KIF13B	ENST00000523968.1	c.*658+160G>A		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77980 AN: 151918 Hom.: 21353 Cov.: 32

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.544

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

GnomAD4 genome AF: 0.513 AC: 78007 AN: 152036 Hom.: 21354 Cov.: 32 AF XY: 0.511 AC XY: 37997 AN XY: 74308

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.565

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.601

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.537

Alfa AF: 0.583 Hom.: 6116

Bravo AF: 0.507

Asia WGS AF: 0.434 AC: 1511 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	5.5
DANN	Benign	0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs12056328; hg19: chr8-29037461; COSMIC: COSV73054452;