10-92632702-A-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004523.4(KIF11):​c.1702+9A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0633 in 1,562,260 control chromosomes in the GnomAD database, including 8,146 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 3604 hom., cov: 32)
Exomes 𝑓: 0.054 ( 4542 hom. )

Consequence

KIF11
NM_004523.4 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.745
Variant links:
Genes affected
KIF11 (HGNC:6388): (kinesin family member 11) This gene encodes a motor protein that belongs to the kinesin-like protein family. Members of this protein family are known to be involved in various kinds of spindle dynamics. The function of this gene product includes chromosome positioning, centrosome separation and establishing a bipolar spindle during cell mitosis. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 10-92632702-A-T is Benign according to our data. Variant chr10-92632702-A-T is described in ClinVar as [Benign]. Clinvar id is 259408.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-92632702-A-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
KIF11NM_004523.4 linkuse as main transcriptc.1702+9A>T intron_variant ENST00000260731.5 NP_004514.2 P52732

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
KIF11ENST00000260731.5 linkuse as main transcriptc.1702+9A>T intron_variant 1 NM_004523.4 ENSP00000260731.3 P52732

Frequencies

GnomAD3 genomes
AF:
0.149
AC:
22672
AN:
151916
Hom.:
3598
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.399
Gnomad AMI
AF:
0.136
Gnomad AMR
AF:
0.122
Gnomad ASJ
AF:
0.0493
Gnomad EAS
AF:
0.0949
Gnomad SAS
AF:
0.0786
Gnomad FIN
AF:
0.00775
Gnomad MID
AF:
0.115
Gnomad NFE
AF:
0.0409
Gnomad OTH
AF:
0.135
GnomAD3 exomes
AF:
0.0804
AC:
18194
AN:
226312
Hom.:
1766
AF XY:
0.0736
AC XY:
9010
AN XY:
122448
show subpopulations
Gnomad AFR exome
AF:
0.410
Gnomad AMR exome
AF:
0.0972
Gnomad ASJ exome
AF:
0.0484
Gnomad EAS exome
AF:
0.115
Gnomad SAS exome
AF:
0.0712
Gnomad FIN exome
AF:
0.00886
Gnomad NFE exome
AF:
0.0411
Gnomad OTH exome
AF:
0.0631
GnomAD4 exome
AF:
0.0540
AC:
76140
AN:
1410226
Hom.:
4542
Cov.:
24
AF XY:
0.0533
AC XY:
37401
AN XY:
701202
show subpopulations
Gnomad4 AFR exome
AF:
0.413
Gnomad4 AMR exome
AF:
0.0946
Gnomad4 ASJ exome
AF:
0.0491
Gnomad4 EAS exome
AF:
0.0895
Gnomad4 SAS exome
AF:
0.0697
Gnomad4 FIN exome
AF:
0.0111
Gnomad4 NFE exome
AF:
0.0407
Gnomad4 OTH exome
AF:
0.0687
GnomAD4 genome
AF:
0.149
AC:
22713
AN:
152034
Hom.:
3604
Cov.:
32
AF XY:
0.144
AC XY:
10736
AN XY:
74320
show subpopulations
Gnomad4 AFR
AF:
0.398
Gnomad4 AMR
AF:
0.122
Gnomad4 ASJ
AF:
0.0493
Gnomad4 EAS
AF:
0.0950
Gnomad4 SAS
AF:
0.0774
Gnomad4 FIN
AF:
0.00775
Gnomad4 NFE
AF:
0.0409
Gnomad4 OTH
AF:
0.134
Alfa
AF:
0.0793
Hom.:
279
Bravo
AF:
0.166
Asia WGS
AF:
0.108
AC:
377
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 31, 2024- -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
9.0
DANN
Benign
0.70
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

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

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

Other links and lift over

dbSNP: rs17107764; hg19: chr10-94392459; COSMIC: COSV53270980; API