8-29205655-T-G

Variant names:

• chr8-29205655-T-G
• rs6991271
• NM_015254.4:c.150-9456A>C

Variant summary

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

The NM_015254.4(KIF13B):​c.150-9456A>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
• Publications: 6 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 = 0.603 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF13B	NM_015254.4	MANE Select	c.150-9456A>C		intron	N/A	NP_056069.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	KIF13B	ENST00000524189.6	TSL:1 MANE Select	c.150-9456A>C		intron	N/A	ENSP00000427900.1
	KIF13B	ENST00000521515.1	TSL:5	c.150-9456A>C		intron	N/A	ENSP00000429201.1
	KIF13B	ENST00000522355.5	TSL:2	n.150-19183A>C		intron	N/A	ENSP00000429027.1

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

African (AFR) AF: 0.409 AC: 16933 AN: 41438

American (AMR) AF: 0.569 AC: 8691 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1788 AN: 3466

East Asian (EAS) AF: 0.336 AC: 1737 AN: 5170

South Asian (SAS) AF: 0.572 AC: 2755 AN: 4820

European-Finnish (FIN) AF: 0.493 AC: 5205 AN: 10562

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.607 AC: 41285 AN: 67966

Other (OTH) AF: 0.547 AC: 1151 AN: 2106

Alfa AF: 0.588 Hom.: 13442

Bravo AF: 0.527

Asia WGS AF: 0.421 AC: 1465 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	2.2
DANN	Benign	0.70
PhyloP100		-0.011
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

Other links and lift over

dbSNP: rs6991271; hg19: chr8-29063172;