rs7007878

chr8-29184936-A-Gchr8-29184936-A-T

Variant summary

Our verdict is Benign. Variant got -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

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 (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF13B	NM_015254.4	c.497+1356T>C		intron_variant		ENST00000524189.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF13B	ENST00000524189.6	c.497+1356T>C		intron_variant		1	NM_015254.4	P1
KIF13B	ENST00000521515.1	c.497+1356T>C		intron_variant		5
KIF13B	ENST00000522355.5	c.*144+1356T>C		intron_variant, NMD_transcript_variant		2
KIF13B	ENST00000523968.1	c.*435+1356T>C		intron_variant, NMD_transcript_variant		5

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

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.511

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.484

Alfa AF: 0.443 Hom.: 30131

Bravo AF: 0.519

Asia WGS AF: 0.365 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.5
Dann	Benign	0.67

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

Publications

LitVar

Other links and lift over

dbSNP: rs7007878; hg19: chr8-29042453;