Variant rs11242122 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.92

Variant links:

Genes affected

KIF3A (HGNC:):

KIF3A links:

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ACMG classification

Classification made for transcript

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	Protein	UniProt
KIF3A	XM_006714526.5 linkuse as main transcript	c.*674G>C		3_prime_UTR_variant	19/19		XP_006714589.1
KIF3A	XM_017008996.3 linkuse as main transcript	c.*674G>C		3_prime_UTR_variant	17/17		XP_016864485.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000431165.1 linkuse as main transcript	n.20+316C>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.599

AC:

91018

AN:

151906

Hom.:

29497

Cov.:

show subpopulations

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.:

AF XY:

0.588

AC XY:

43700

AN XY:

74290

show subpopulations

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

DANN

Benign

0.74

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over