Genetic Variant KIF3A:c.-368C>A (chr5-132737787-G-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001300791.2(KIF3A):c.-368C>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

KIF3A
NM_001300791.2 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.520

Publications

1 publications found

Variant links:

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]

KIF3A links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KIF3A	NM_001300791.2 link	c.-368C>A		upstream_gene_variant		ENST00000403231.6	NP_001287720.1	Q9Y496E9PES4B4DHG8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
KIF3A	ENST00000403231.6 link	c.-368C>A	upstream_gene_variant	2	NM_001300791.2	ENSP00000385808.1	E9PES4
KIF3A	ENST00000378735.5 link	c.-368C>A	upstream_gene_variant	1		ENSP00000368009.1	J3KPF9
KIF3A	ENST00000618515.4 link	c.-368C>A	upstream_gene_variant	5		ENSP00000483023.1	A0A087X011
KIF3A	ENST00000378746.8 link	c.-368C>A	upstream_gene_variant	5		ENSP00000368020.3	Q9Y496

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

233668

Hom.:

AF XY:

0.00

AC XY:

AN XY:

119370

African (AFR)

AF:

0.00

AC:

AN:

6494

American (AMR)

AF:

0.00

AC:

AN:

6440

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

8676

East Asian (EAS)

AF:

0.00

AC:

AN:

19126

South Asian (SAS)

AF:

0.00

AC:

AN:

8222

European-Finnish (FIN)

AF:

0.00

AC:

AN:

19384

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1184

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

148642

Other (OTH)

AF:

0.00

AC:

AN:

15500

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

0.75

(source)

DANN

Benign

0.52

PhyloP100

-0.52

PromoterAI

-0.040

Neutral

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over