GeneBe

rs3840030

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_198525.3(KIF7):​c.2719-20_2719-13delCCCTCCCT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000104 in 963,520 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)
Exomes 𝑓: 0.0000010 ( 0 hom. )

Consequence

KIF7
NM_198525.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.60

Publications

1 publications found
Variant links:
Genes affected
KIF7 (HGNC:30497): (kinesin family member 7) This gene encodes a cilia-associated protein belonging to the kinesin family. This protein plays a role in the sonic hedgehog (SHH) signaling pathway through the regulation of GLI transcription factors. It functions as a negative regulator of the SHH pathway by preventing inappropriate activation of GLI2 in the absence of ligand, and as a positive regulator by preventing the processing of GLI3 into its repressor form. Mutations in this gene have been associated with various ciliopathies. [provided by RefSeq, Oct 2011]
KIF7 Gene-Disease associations (from GenCC):
  • acrocallosal syndrome
    Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae), Orphanet
  • neurodevelopmental disorder
    Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
  • hydrolethalus syndrome 2
    Inheritance: AR Classification: STRONG, MODERATE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
  • hydrolethalus syndrome
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • multiple epiphyseal dysplasia, Al-Gazali type
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • orofaciodigital syndrome type 6
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198525.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
KIF7
NM_198525.3
MANE Select
c.2719-20_2719-13delCCCTCCCT
intron
N/ANP_940927.2Q2M1P5

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
KIF7
ENST00000394412.8
TSL:5 MANE Select
c.2719-20_2719-13delCCCTCCCT
intron
N/AENSP00000377934.3Q2M1P5
KIF7
ENST00000696512.1
c.2842-20_2842-13delCCCTCCCT
intron
N/AENSP00000512678.1A0A8Q3SIQ8
KIF7
ENST00000946200.1
c.2731-20_2731-13delCCCTCCCT
intron
N/AENSP00000616259.1

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000104
AC:
1
AN:
963520
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
494350
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
24772
American (AMR)
AF:
0.00
AC:
0
AN:
39358
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
21722
East Asian (EAS)
AF:
0.00
AC:
0
AN:
35714
South Asian (SAS)
AF:
0.00
AC:
0
AN:
73754
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
38376
Middle Eastern (MID)
AF:
0.000218
AC:
1
AN:
4594
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
680878
Other (OTH)
AF:
0.00
AC:
0
AN:
44352
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
Cov.:
0
Alfa
AF:
0.00
Hom.:
1558

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.6

Splicing

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

Publications

Other links and lift over

dbSNP: rs3840030; hg19: chr15-90176239; API