8-29097375-T-G

Variant names:

• chr8-29097375-T-G
• rs7844537
• NM_015254.4:c.4324+1758A>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.4324+1758A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,180 control chromosomes in the GnomAD database, including 58,044 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 0.87 (58044 hom., cov: 31)
• Consequence: KIF13B NM_015254.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.698
• Publications: 3 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=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.927 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.4324+1758A>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.4324+1758A>C		intron	N/A	ENSP00000427900.1
	KIF13B	ENST00000523130.1	TSL:5	c.163+1758A>C		intron	N/A	ENSP00000429106.1

Frequencies

GnomAD3 genomes AF: 0.869 AC: 132141 AN: 152062 Hom.: 58003 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.859

Gnomad ASJ AF: 0.920

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.838

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.869 AC: 132243 AN: 152180 Hom.: 58044 Cov.: 31 AF XY: 0.866 AC XY: 64398 AN XY: 74400

African (AFR) AF: 0.791 AC: 32799 AN: 41486

American (AMR) AF: 0.860 AC: 13154 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.920 AC: 3195 AN: 3472

East Asian (EAS) AF: 0.557 AC: 2876 AN: 5164

South Asian (SAS) AF: 0.837 AC: 4040 AN: 4826

European-Finnish (FIN) AF: 0.922 AC: 9768 AN: 10594

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.933 AC: 63464 AN: 68018

Other (OTH) AF: 0.880 AC: 1858 AN: 2112

Alfa AF: 0.908 Hom.: 136162

Bravo AF: 0.860

Asia WGS AF: 0.714 AC: 2484 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.47
DANN	Benign	0.39
PhyloP100		-0.70
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: rs7844537; hg19: chr8-28954892;