8-29184936-A-G

Variant names:

• chr8-29184936-A-G
• rs7007878
• NM_015254.4:c.497+1356T>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.497+1356T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,788 control chromosomes in the GnomAD database, including 21,290 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 (21290 hom., cov: 30)
• Consequence: KIF13B NM_015254.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148
• Publications: 5 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 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.497+1356T>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.497+1356T>C		intron	N/A	ENSP00000427900.1
	KIF13B	ENST00000521515.1	TSL:5	c.497+1356T>C		intron	N/A	ENSP00000429201.1
	KIF13B	ENST00000522355.5	TSL:2	n.*144+1356T>C		intron	N/A	ENSP00000429027.1

Frequencies

GnomAD3 genomes AF: 0.514 AC: 77897 AN: 151670 Hom.: 21245 Cov.: 30

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.511

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.514 AC: 78017 AN: 151788 Hom.: 21290 Cov.: 30 AF XY: 0.513 AC XY: 38079 AN XY: 74174

African (AFR) AF: 0.691 AC: 28579 AN: 41358

American (AMR) AF: 0.511 AC: 7797 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1755 AN: 3470

East Asian (EAS) AF: 0.204 AC: 1054 AN: 5162

South Asian (SAS) AF: 0.396 AC: 1899 AN: 4798

European-Finnish (FIN) AF: 0.541 AC: 5702 AN: 10532

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29681 AN: 67906

Other (OTH) AF: 0.484 AC: 1020 AN: 2106

Alfa AF: 0.454 Hom.: 68404

Bravo AF: 0.519

Asia WGS AF: 0.365 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
DANN	Benign	0.67
PhyloP100		-0.15
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs7007878; hg19: chr8-29042453;