rs1466627

chr8-29113348-C-Gchr8-29113348-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.3930+115G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 551,204 control chromosomes in the GnomAD database, including 63,761 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 0.43 (15181 hom., cov: 33)
  • Exomes 𝑓: 0.48 (48580 hom.)
• Consequence: KIF13B NM_015254.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.856

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF13B	NM_015254.4	c.3930+115G>C		intron_variant		ENST00000524189.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF13B	ENST00000524189.6	c.3930+115G>C		intron_variant		1	NM_015254.4	P1
	ENST00000523661.1	n.98+2678C>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64903 AN: 152040 Hom.: 15187 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.443

GnomAD4 exome AF: 0.479 AC: 191171 AN: 399046 Hom.: 48580 AF XY: 0.478 AC XY: 99937 AN XY: 209178

Gnomad4 AFR exome AF: 0.255

Gnomad4 AMR exome AF: 0.346

Gnomad4 ASJ exome AF: 0.479

Gnomad4 EAS exome AF: 0.213

Gnomad4 SAS exome AF: 0.408

Gnomad4 FIN exome AF: 0.498

Gnomad4 NFE exome AF: 0.531

Gnomad4 OTH exome AF: 0.475

GnomAD4 genome AF: 0.427 AC: 64921 AN: 152158 Hom.: 15181 Cov.: 33 AF XY: 0.424 AC XY: 31563 AN XY: 74376

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.419

Gnomad4 FIN AF: 0.504

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.437

Alfa AF: 0.473 Hom.: 2209

Bravo AF: 0.410

Asia WGS AF: 0.311 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.15
Dann	Benign	0.53

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

Publications

LitVar

Other links and lift over

dbSNP: rs1466627; hg19: chr8-28970865;