chr16-57746491-G-A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_005886.3(KATNB1):​c.289+1980G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0972 in 152,260 control chromosomes in the GnomAD database, including 897 homozygotes. 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 0.097 ( 897 hom., cov: 32)

Consequence

KATNB1
NM_005886.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.65

Publications

3 publications found
Variant links:
Genes affected
KATNB1 (HGNC:6217): (katanin regulatory subunit B1) Microtubules, polymers of alpha and beta tubulin subunits, form the mitotic spindle of a dividing cell and help to organize membranous organelles during interphase. Katanin is a heterodimer that consists of a 60 kDa ATPase (p60 subunit A 1) and an 80 kDa accessory protein (p80 subunit B 1). The p60 subunit acts to sever and disassemble microtubules, while the p80 subunit targets the enzyme to the centrosome. Katanin is a member of the AAA family of ATPases. [provided by RefSeq, Jul 2008]
KATNB1 Gene-Disease associations (from GenCC):
  • lissencephaly 6 with microcephaly
    Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: PanelApp Australia, Ambry Genetics, Labcorp Genetics (formerly Invitae), Illumina, G2P
  • microlissencephaly
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KATNB1NM_005886.3 linkc.289+1980G>A intron_variant Intron 4 of 19 ENST00000379661.8 NP_005877.2 Q9BVA0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KATNB1ENST00000379661.8 linkc.289+1980G>A intron_variant Intron 4 of 19 5 NM_005886.3 ENSP00000368982.3 Q9BVA0

Frequencies

GnomAD3 genomes
AF:
0.0972
AC:
14792
AN:
152142
Hom.:
894
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.160
Gnomad AMI
AF:
0.0175
Gnomad AMR
AF:
0.0535
Gnomad ASJ
AF:
0.0648
Gnomad EAS
AF:
0.0523
Gnomad SAS
AF:
0.137
Gnomad FIN
AF:
0.0427
Gnomad MID
AF:
0.0665
Gnomad NFE
AF:
0.0811
Gnomad OTH
AF:
0.0805
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0972
AC:
14807
AN:
152260
Hom.:
897
Cov.:
32
AF XY:
0.0949
AC XY:
7062
AN XY:
74450
show subpopulations
African (AFR)
AF:
0.160
AC:
6661
AN:
41536
American (AMR)
AF:
0.0533
AC:
816
AN:
15304
Ashkenazi Jewish (ASJ)
AF:
0.0648
AC:
225
AN:
3472
East Asian (EAS)
AF:
0.0520
AC:
270
AN:
5188
South Asian (SAS)
AF:
0.137
AC:
662
AN:
4830
European-Finnish (FIN)
AF:
0.0427
AC:
453
AN:
10604
Middle Eastern (MID)
AF:
0.0714
AC:
21
AN:
294
European-Non Finnish (NFE)
AF:
0.0811
AC:
5515
AN:
68010
Other (OTH)
AF:
0.0796
AC:
168
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
687
1374
2060
2747
3434
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
182
364
546
728
910
<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:
0.0420
Hom.:
29
Bravo
AF:
0.0988
Asia WGS
AF:
0.0890
AC:
314
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
1.7
DANN
Benign
0.87
PhyloP100
-1.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs12708992; hg19: chr16-57780403; API