GeneBe

rs1736656

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.82 ( 26161 hom., 26471 hem., cov: 22)
Exomes 𝑓: 0.86 ( 76950 hom. 85623 hem. )
Failed GnomAD Quality Control

Consequence

KIF4CP
intragenic

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.43

Publications

2 publications found
Variant links:
Genes affected
KIF4CP (HGNC:13340): (kinesin family member 4C, pseudogene)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KIF4CP n.79323946C>A intragenic_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KIF4CPENST00000422742.2 linkn.418-81C>A intron_variant Intron 1 of 2 6

Frequencies

GnomAD3 genomes
AF:
0.820
AC:
89829
AN:
109602
Hom.:
26162
Cov.:
22
show subpopulations
Gnomad AFR
AF:
0.701
Gnomad AMI
AF:
0.854
Gnomad AMR
AF:
0.823
Gnomad ASJ
AF:
0.913
Gnomad EAS
AF:
0.997
Gnomad SAS
AF:
0.822
Gnomad FIN
AF:
0.867
Gnomad MID
AF:
0.903
Gnomad NFE
AF:
0.863
Gnomad OTH
AF:
0.853
GnomAD4 exome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.861
AC:
263743
AN:
306364
Hom.:
76950
Cov.:
3
AF XY:
0.862
AC XY:
85623
AN XY:
99292
show subpopulations
African (AFR)
AF:
0.699
AC:
6350
AN:
9082
American (AMR)
AF:
0.776
AC:
10585
AN:
13647
Ashkenazi Jewish (ASJ)
AF:
0.911
AC:
8092
AN:
8881
East Asian (EAS)
AF:
0.999
AC:
20515
AN:
20542
South Asian (SAS)
AF:
0.841
AC:
20256
AN:
24093
European-Finnish (FIN)
AF:
0.861
AC:
22636
AN:
26282
Middle Eastern (MID)
AF:
0.903
AC:
1311
AN:
1452
European-Non Finnish (NFE)
AF:
0.860
AC:
158765
AN:
184643
Other (OTH)
AF:
0.859
AC:
15233
AN:
17742
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.491
Heterozygous variant carriers
0
1103
2206
3310
4413
5516
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
798
1596
2394
3192
3990
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Data not reliable, filtered out with message: InbreedingCoeff
AF:
0.820
AC:
89870
AN:
109658
Hom.:
26161
Cov.:
22
AF XY:
0.830
AC XY:
26471
AN XY:
31910
show subpopulations
African (AFR)
AF:
0.701
AC:
21027
AN:
29993
American (AMR)
AF:
0.823
AC:
8482
AN:
10307
Ashkenazi Jewish (ASJ)
AF:
0.913
AC:
2398
AN:
2627
East Asian (EAS)
AF:
0.997
AC:
3490
AN:
3499
South Asian (SAS)
AF:
0.825
AC:
2070
AN:
2510
European-Finnish (FIN)
AF:
0.867
AC:
4841
AN:
5583
Middle Eastern (MID)
AF:
0.903
AC:
195
AN:
216
European-Non Finnish (NFE)
AF:
0.863
AC:
45510
AN:
52751
Other (OTH)
AF:
0.855
AC:
1278
AN:
1494
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.512
Heterozygous variant carriers
0
564
1127
1691
2254
2818
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
752
1504
2256
3008
3760
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.846
Hom.:
7257
Bravo
AF:
0.809

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.53
DANN
Benign
0.14
PhyloP100
-1.4

Splicing

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

Publications

Other links and lift over

dbSNP: rs1736656; hg19: chrX-78579443; API