rs12186803

Variant names:

• chr5-132704377-G-A
• rs12186803
• NM_001300791.2:c.1310-758C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-132704377-G-A
• chr5-132704377-G-C

Variant summary

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

The NM_001300791.2(KIF3A):​c.1310-758C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 151,552 control chromosomes in the GnomAD database, including 6,979 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 0.27 (6979 hom., cov: 32)
• Consequence: KIF3A NM_001300791.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405
• Publications: 24 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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.1310-758C>T		intron_variant	Intron 11 of 18	ENST00000403231.6	NP_001287720.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KIF3A	ENST00000403231.6	c.1310-758C>T		intron_variant	Intron 11 of 18	2	NM_001300791.2	ENSP00000385808.1

Frequencies

GnomAD3 genomes AF: 0.266 AC: 40216 AN: 151434 Hom.: 6977 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.266 AC: 40253 AN: 151552 Hom.: 6979 Cov.: 32 AF XY: 0.275 AC XY: 20386 AN XY: 74026

African (AFR) AF: 0.388 AC: 16047 AN: 41374

American (AMR) AF: 0.299 AC: 4547 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 522 AN: 3464

East Asian (EAS) AF: 0.753 AC: 3888 AN: 5160

South Asian (SAS) AF: 0.182 AC: 876 AN: 4822

European-Finnish (FIN) AF: 0.357 AC: 3748 AN: 10496

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.149 AC: 10109 AN: 67700

Other (OTH) AF: 0.220 AC: 464 AN: 2106

Alfa AF: 0.176 Hom.: 7164

Bravo AF: 0.272

Asia WGS AF: 0.440 AC: 1529 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.84
DANN	Benign	0.60
PhyloP100		-0.41
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: rs12186803; hg19: chr5-132040069;