rs12056328

Variant names:

• chr8-29179944-C-T
• rs12056328
• NM_015254.4:c.720+160G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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 (NFE) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015254.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF13B	NM_015254.4	MANE Select	c.720+160G>A		intron	N/A	NP_056069.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF13B	ENST00000524189.6	TSL:1 MANE Select	c.720+160G>A		intron	N/A	ENSP00000427900.1	Q9NQT8-1
	KIF13B	ENST00000521515.1	TSL:5	c.720+160G>A		intron	N/A	ENSP00000429201.1	E7ERX9
	KIF13B	ENST00000522355.5	TSL:2	n.*367+160G>A		intron	N/A	ENSP00000429027.1	F2Z2F9

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

African (AFR) AF: 0.324 AC: 13460 AN: 41480

American (AMR) AF: 0.565 AC: 8631 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1843 AN: 3462

East Asian (EAS) AF: 0.339 AC: 1753 AN: 5176

South Asian (SAS) AF: 0.601 AC: 2896 AN: 4816

European-Finnish (FIN) AF: 0.506 AC: 5340 AN: 10550

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42163 AN: 67974

Other (OTH) AF: 0.537 AC: 1131 AN: 2108

Alfa AF: 0.593 Hom.: 11762

Bravo AF: 0.507

Asia WGS AF: 0.434 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.5
DANN	Benign	0.71
PhyloP100		1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12056328; hg19: chr8-29037461; COSMIC: COSV73054452;