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9-114091903-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001388308.1(KIF12):c.1914T>C(p.Ser638=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0248 in 1,611,524 control chromosomes in the GnomAD database, including 645 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.021 ( 39 hom., cov: 32)
Exomes 𝑓: 0.025 ( 606 hom. )

Consequence

KIF12
NM_001388308.1 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.97
Variant links:
Genes affected
KIF12 (HGNC:21495): (kinesin family member 12) This gene encodes a member of the kinesin superfamily of microtubule-associated molecular motors with functions related to the microtubule cytosekelton. Members of this superfamily play important roles in intracellular transport and cell division. A similar protein in mouse functions in the beta cell antioxidant signaling cascade, acting as a scaffold for the transcription factor specificity protein 1 (Sp1). Mice that lack this gene exhibit beta cell oxidative stress resulting in hypoinsulinemic glucose intolerance. [provided by RefSeq, Jul 2016]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 9-114091903-A-G is Benign according to our data. Variant chr9-114091903-A-G is described in ClinVar as [Benign]. Clinvar id is 2037464.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.97 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0595 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KIF12NM_001388308.1 linkuse as main transcriptc.1914T>C p.Ser638= synonymous_variant 19/19 ENST00000640217.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KIF12ENST00000640217.2 linkuse as main transcriptc.1914T>C p.Ser638= synonymous_variant 19/195 NM_001388308.1 P1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0209
AC:
3184
AN:
151996
Hom.:
39
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00495
Gnomad AMI
AF:
0.0186
Gnomad AMR
AF:
0.0257
Gnomad ASJ
AF:
0.0790
Gnomad EAS
AF:
0.000387
Gnomad SAS
AF:
0.0116
Gnomad FIN
AF:
0.0291
Gnomad MID
AF:
0.0633
Gnomad NFE
AF:
0.0272
Gnomad OTH
AF:
0.0307
GnomAD3 exomes
AF:
0.0222
AC:
5505
AN:
247856
Hom.:
117
AF XY:
0.0226
AC XY:
3039
AN XY:
134532
show subpopulations
Gnomad AFR exome
AF:
0.00379
Gnomad AMR exome
AF:
0.0130
Gnomad ASJ exome
AF:
0.0872
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.0115
Gnomad FIN exome
AF:
0.0234
Gnomad NFE exome
AF:
0.0281
Gnomad OTH exome
AF:
0.0248
GnomAD4 exome
AF:
0.0252
AC:
36756
AN:
1459410
Hom.:
606
Cov.:
31
AF XY:
0.0250
AC XY:
18158
AN XY:
725678
show subpopulations
Gnomad4 AFR exome
AF:
0.00565
Gnomad4 AMR exome
AF:
0.0143
Gnomad4 ASJ exome
AF:
0.0861
Gnomad4 EAS exome
AF:
0.000101
Gnomad4 SAS exome
AF:
0.0124
Gnomad4 FIN exome
AF:
0.0205
Gnomad4 NFE exome
AF:
0.0265
Gnomad4 OTH exome
AF:
0.0282
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.0209
AC:
3184
AN:
152114
Hom.:
39
Cov.:
32
AF XY:
0.0209
AC XY:
1551
AN XY:
74352
show subpopulations
Gnomad4 AFR
AF:
0.00496
Gnomad4 AMR
AF:
0.0256
Gnomad4 ASJ
AF:
0.0790
Gnomad4 EAS
AF:
0.000388
Gnomad4 SAS
AF:
0.0119
Gnomad4 FIN
AF:
0.0291
Gnomad4 NFE
AF:
0.0272
Gnomad4 OTH
AF:
0.0304
Alfa
AF:
0.0266
Hom.:
40
Bravo
AF:
0.0208
Asia WGS
AF:
0.00549
AC:
19
AN:
3478
EpiCase
AF:
0.0345
EpiControl
AF:
0.0321

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingInvitaeJan 25, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
Cadd
Benign
0.20
Dann
Benign
0.41
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0

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: rs117751044; hg19: chr9-116854183; COSMIC: COSV65118486; COSMIC: COSV65118486; API