rs11242122

Variant names:

• chr5-132689016-C-G
• rs11242122
• XM_006714526.5:c.*674G>C

Your query was ambiguous. Multiple possible variants found:

• chr5-132689016-C-G
• chr5-132689016-C-T

Variant summary

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

The XM_006714526.5(KIF3A):​c.*674G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,024 control chromosomes in the GnomAD database, including 29,499 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 0.60 (29499 hom., cov: 32)
• Consequence: KIF3A XM_006714526.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.92
• 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF3A	XM_006714526.5	c.*674G>C		3_prime_UTR_variant	Exon 19 of 19		XP_006714589.1
KIF3A	XM_017008996.3	c.*674G>C		3_prime_UTR_variant	Exon 17 of 17		XP_016864485.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230612	ENST00000431165.1	n.20+316C>G		intron_variant	Intron 1 of 2	5

Frequencies

GnomAD3 genomes AF: 0.599 AC: 91018 AN: 151906 Hom.: 29497 Cov.: 32

Gnomad AFR AF: 0.417

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.626

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

GnomAD4 genome AF: 0.599 AC: 91045 AN: 152024 Hom.: 29499 Cov.: 32 AF XY: 0.588 AC XY: 43700 AN XY: 74290

African (AFR) AF: 0.416 AC: 17257 AN: 41462

American (AMR) AF: 0.563 AC: 8601 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2385 AN: 3470

East Asian (EAS) AF: 0.162 AC: 836 AN: 5172

South Asian (SAS) AF: 0.649 AC: 3129 AN: 4820

European-Finnish (FIN) AF: 0.543 AC: 5715 AN: 10534

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.747 AC: 50784 AN: 67974

Other (OTH) AF: 0.624 AC: 1318 AN: 2112

Alfa AF: 0.652 Hom.: 3985

Bravo AF: 0.586

Asia WGS AF: 0.448 AC: 1560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	18
DANN	Benign	0.74
PhyloP100		1.9

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11242122; hg19: chr5-132024708; COSMIC: COSV66439650;