5-132710020-C-T

Variant names:

• chr5-132710020-C-T
• rs12514685
• NM_001300791.2:c.1228+939G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001300791.2(KIF3A):​c.1228+939G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,974 control chromosomes in the GnomAD database, including 10,989 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 0.32 (10989 hom., cov: 32)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 7 publications found

Genes affected

KIF3A (HGNC:6319): (kinesin family member 3A) Enables protein phosphatase binding activity; small GTPase binding activity; and spectrin binding activity. Involved in protein localization to cell junction and protein transport. Located in centriole and centrosome. Part of kinesin II complex. Colocalizes with spindle microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000230612 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF3A	NM_001300791.2	c.1228+939G>A		intron_variant	Intron 9 of 18	ENST00000403231.6	NP_001287720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF3A	ENST00000403231.6	c.1228+939G>A		intron_variant	Intron 9 of 18	2	NM_001300791.2	ENSP00000385808.1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48818 AN: 151856 Hom.: 10958 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.0165

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.258

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

GnomAD4 genome AF: 0.322 AC: 48907 AN: 151974 Hom.: 10989 Cov.: 32 AF XY: 0.331 AC XY: 24555 AN XY: 74256

African (AFR) AF: 0.580 AC: 24062 AN: 41464

American (AMR) AF: 0.324 AC: 4950 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3900 AN: 5176

South Asian (SAS) AF: 0.181 AC: 874 AN: 4818

European-Finnish (FIN) AF: 0.358 AC: 3758 AN: 10500

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10231 AN: 67958

Other (OTH) AF: 0.262 AC: 552 AN: 2108

Alfa AF: 0.139 Hom.: 323

Bravo AF: 0.337

Asia WGS AF: 0.457 AC: 1585 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
CADD	Benign	16
DANN	Benign	0.75
PhyloP100		0.14
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: rs12514685; hg19: chr5-132045712;