GeneBe

6-97010244-G-GAAGC

Variant names:

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000620278.1(KLHL32):​c.-653_-652insAGCA variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.65 ( 33894 hom., cov: 0)
Exomes 𝑓: 0.70 ( 5 hom. )

Consequence

KLHL32
ENST00000620278.1 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04

Publications

4 publications found
Variant links:
Genes affected
KLHL32 (HGNC:21221): (kelch like family member 32)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.883 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KLHL32NM_052904.4 linkc.205-31247_205-31246insAGCA intron_variant Intron 3 of 10 ENST00000369261.9 NP_443136.2 Q96NJ5-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KLHL32ENST00000369261.9 linkc.205-31247_205-31246insAGCA intron_variant Intron 3 of 10 2 NM_052904.4 ENSP00000358265.4 Q96NJ5-1

Frequencies

GnomAD3 genomes
AF:
0.650
AC:
98384
AN:
151358
Hom.:
33834
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.890
Gnomad AMI
AF:
0.483
Gnomad AMR
AF:
0.671
Gnomad ASJ
AF:
0.577
Gnomad EAS
AF:
0.601
Gnomad SAS
AF:
0.697
Gnomad FIN
AF:
0.523
Gnomad MID
AF:
0.580
Gnomad NFE
AF:
0.526
Gnomad OTH
AF:
0.636
GnomAD4 exome
AF:
0.700
AC:
14
AN:
20
Hom.:
5
Cov.:
0
AF XY:
0.667
AC XY:
12
AN XY:
18
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AF:
1.00
AC:
2
AN:
2
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.500
AC:
4
AN:
8
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.833
AC:
5
AN:
6
Other (OTH)
AF:
0.750
AC:
3
AN:
4
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.438
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Hom
Variant carriers
0
2
4
6
8
10
<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
AF:
0.650
AC:
98505
AN:
151474
Hom.:
33894
Cov.:
0
AF XY:
0.651
AC XY:
48175
AN XY:
73960
show subpopulations
African (AFR)
AF:
0.890
AC:
36784
AN:
41322
American (AMR)
AF:
0.672
AC:
10241
AN:
15240
Ashkenazi Jewish (ASJ)
AF:
0.577
AC:
1997
AN:
3462
East Asian (EAS)
AF:
0.600
AC:
3082
AN:
5134
South Asian (SAS)
AF:
0.696
AC:
3341
AN:
4798
European-Finnish (FIN)
AF:
0.523
AC:
5447
AN:
10412
Middle Eastern (MID)
AF:
0.579
AC:
169
AN:
292
European-Non Finnish (NFE)
AF:
0.526
AC:
35671
AN:
67810
Other (OTH)
AF:
0.636
AC:
1334
AN:
2096
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.510
Heterozygous variant carriers
0
1567
3134
4701
6268
7835
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
764
1528
2292
3056
3820
<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:
0.572
Hom.:
2737
Asia WGS
AF:
0.701
AC:
2439
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
-1.0
Mutation Taster
=100/0
polymorphism (auto)

Splicing

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

Publications

Other links and lift over

dbSNP: rs2307652; hg19: chr6-97458120; API