5-62306184-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The ENST00000401507.7(KIF2A):c.-289G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00817 in 315,732 control chromosomes in the GnomAD database, including 63 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.015 (52 hom., cov: 33)
  • Exomes 𝑓: 0.0020 (11 hom.)
• Consequence: KIF2A ENST00000401507.7 5_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.417

Genes affected

KIF2A (HGNC:6318): (kinesin family member 2A) The protein encoded by this gene is a plus end-directed motor required for normal mitotic progression. The encoded protein is required for normal spindle activity during mitosis and is necessary for normal brain development. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 5-62306184-G-A is Benign according to our data. Variant chr5-62306184-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1204563.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0148 (2256/152176) while in subpopulation AFR AF= 0.0515 (2138/41542). AF 95% confidence interval is 0.0496. There are 52 homozygotes in gnomad4. There are 1016 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High AC in GnomAd at 2249 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KIF2A	NM_001098511.3			upstream_gene_variant		ENST00000407818.8
KIF2A	NM_001243952.2			upstream_gene_variant
KIF2A	NM_001243953.2			upstream_gene_variant
KIF2A	NM_004520.5			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KIF2A	ENST00000407818.8			upstream_gene_variant		1	NM_001098511.3	A1

Frequencies

GnomAD3 genomes AF: 0.0148 AC: 2249 AN: 152068 Hom.: 52 Cov.: 33

Gnomad AFR AF: 0.0514

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00596

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000132

Gnomad OTH AF: 0.00860

GnomAD4 exome AF: 0.00198 AC: 324 AN: 163556 Hom.: 11 Cov.: 0 AF XY: 0.00164 AC XY: 136 AN XY: 83170

Gnomad4 AFR exome AF: 0.0508

Gnomad4 AMR exome AF: 0.00553

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000337

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000853

Gnomad4 OTH exome AF: 0.00589

GnomAD4 genome AF: 0.0148 AC: 2256 AN: 152176 Hom.: 52 Cov.: 33 AF XY: 0.0137 AC XY: 1016 AN XY: 74406

Gnomad4 AFR AF: 0.0515

Gnomad4 AMR AF: 0.00595

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000132

Gnomad4 OTH AF: 0.00851

Alfa AF: 0.00177 Hom.: 0

Bravo AF: 0.0171

Asia WGS AF: 0.00466 AC: 16 AN: 3446

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Sep 18, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	14
Dann	Benign	0.90

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

Publications

LitVar

Other links and lift over

dbSNP: rs146315657; hg19: chr5-61602011;