rs11242122

chr5-132689016-C-Gchr5-132689016-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

KIF3A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
KIF3A	XM_006714526.5	c.*674G>C		3_prime_UTR_variant	19/19
KIF3A	XM_017008996.3	c.*674G>C		3_prime_UTR_variant	17/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000431165.1	n.20+316C>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.416

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.624

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

Splicing

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

Publications

LitVar

Other links and lift over

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