rs2954793

Variant names:

• chr8-29248542-C-T
• rs2954793
• NM_015254.4:c.56-3103G>A

Variant summary

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

The NM_015254.4(KIF13B):​c.56-3103G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,086 control chromosomes in the GnomAD database, including 5,974 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 0.28 (5974 hom., cov: 32)
• Consequence: KIF13B NM_015254.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42
• 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF13B	NM_015254.4	c.56-3103G>A		intron_variant	Intron 1 of 39	ENST00000524189.6	NP_056069.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF13B	ENST00000524189.6	c.56-3103G>A		intron_variant	Intron 1 of 39	1	NM_015254.4	ENSP00000427900.1

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41855 AN: 151968 Hom.: 5963 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.0699

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.276 AC: 41920 AN: 152086 Hom.: 5974 Cov.: 32 AF XY: 0.276 AC XY: 20511 AN XY: 74360

African (AFR) AF: 0.316 AC: 13092 AN: 41460

American (AMR) AF: 0.258 AC: 3945 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1245 AN: 3472

East Asian (EAS) AF: 0.0696 AC: 361 AN: 5184

South Asian (SAS) AF: 0.186 AC: 897 AN: 4820

European-Finnish (FIN) AF: 0.369 AC: 3903 AN: 10568

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17618 AN: 67978

Other (OTH) AF: 0.259 AC: 547 AN: 2112

Alfa AF: 0.263 Hom.: 2191

Bravo AF: 0.268

Asia WGS AF: 0.170 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.31
DANN	Benign	0.31
PhyloP100		-2.4
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: rs2954793; hg19: chr8-29106059;