5-62352567-ATTT-ATT

Position:

• chr5-62352567-ATTT-ATT

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001098511.3(KIF2A):​c.335-9delT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0567 in 929,956 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.00032 (0 hom., cov: 32)
  • Exomes 𝑓: 0.067 (0 hom.)
• Consequence: KIF2A NM_001098511.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.330

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]

ENSG00000288643 (HGNC:):

DIMT1 (HGNC:30217): (DIM1 rRNA methyltransferase and ribosome maturation factor) The protein encoded by this gene is a methyltransferase that is responsible for dimethylation of adjacent adenosines near the 18S rRNA decoding site. The encoded protein is essential for ribosome biogenesis, although its catalytic activity is not involved in the process. The yeast ortholog of this protein functions in the cytoplasm while this protein functions in the nucleus. [provided by RefSeq, Jan 2017]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 5-62352567-AT-A is Benign according to our data. Variant chr5-62352567-AT-A is described in ClinVar as [Benign]. Clinvar id is 1599889.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KIF2A	NM_001098511.3	c.335-9delT		intron_variant		ENST00000407818.8	NP_001091981.1
KIF2A	NM_004520.5	c.335-9delT		intron_variant			NP_004511.2
KIF2A	NM_001243953.2	c.335-9delT		intron_variant			NP_001230882.1
KIF2A	NM_001243952.2	c.254-9delT		intron_variant			NP_001230881.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KIF2A	ENST00000407818.8	c.335-9delT		intron_variant		1	NM_001098511.3	ENSP00000385000.3
ENSG00000288643	ENST00000509663.2	n.64+46043delT		intron_variant		3		ENSP00000502199.1

Frequencies

GnomAD3 genomes AF: 0.000311 AC: 46 AN: 147980 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000419

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000338

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00105

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000210

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0674 AC: 52706 AN: 781906 Hom.: 0 Cov.: 17 AF XY: 0.0690 AC XY: 26485 AN XY: 384102

Gnomad4 AFR exome AF: 0.0666

Gnomad4 AMR exome AF: 0.0963

Gnomad4 ASJ exome AF: 0.0950

Gnomad4 EAS exome AF: 0.0857

Gnomad4 SAS exome AF: 0.0921

Gnomad4 FIN exome AF: 0.0618

Gnomad4 NFE exome AF: 0.0639

Gnomad4 OTH exome AF: 0.0734

GnomAD4 genome AF: 0.000317 AC: 47 AN: 148050 Hom.: 0 Cov.: 32 AF XY: 0.000375 AC XY: 27 AN XY: 72064

Gnomad4 AFR AF: 0.000443

Gnomad4 AMR AF: 0.000338

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00105

Gnomad4 NFE AF: 0.000210

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 24, 2023

- -

Computational scores

Source: dbNSFP v4.3

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: rs762620321; hg19: chr5-61648394;