Variant chr16-57737214-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_005886.3(KATNB1):c.-30G>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 1,612,890 control chromosomes in the GnomAD database, including 16,466 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1641 hom., cov: 33)

Exomes 𝑓: 0.14 ( 14825 hom. )

Consequence

KATNB1
NM_005886.3 5_prime_UTR_premature_start_codon_gain

Scores

Splicing: ADA: 0.0003640

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.27

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 links:

KATNB1 (HGNC:):

KATNB1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant 16-57737214-G-T is Benign according to our data. Variant chr16-57737214-G-T is described in ClinVar as [Benign]. Clinvar id is 1286789.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KATNB1	NM_005886.3 linkuse as main transcript	c.-30G>T		5_prime_UTR_premature_start_codon_gain_variant	2/20	ENST00000379661.8	NP_005877.2	Q9BVA0
KATNB1	NM_005886.3 linkuse as main transcript	c.-30G>T		5_prime_UTR_variant	2/20	ENST00000379661.8	NP_005877.2	Q9BVA0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KATNB1	ENST00000379661 linkuse as main transcript	c.-30G>T		5_prime_UTR_premature_start_codon_gain_variant	2/20	5	NM_005886.3	ENSP00000368982.3		Q9BVA0
KATNB1	ENST00000379661 linkuse as main transcript	c.-30G>T		5_prime_UTR_variant	2/20	5	NM_005886.3	ENSP00000368982.3		Q9BVA0

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21407

AN:

152156

Hom.:

1641

Cov.:

show subpopulations

Gnomad AFR

AF:

0.183

Gnomad AMI

AF:

0.122

Gnomad AMR

AF:

0.102

Gnomad ASJ

AF:

0.186

Gnomad EAS

AF:

0.000962

Gnomad SAS

AF:

0.0923

Gnomad FIN

AF:

0.0930

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.143

Gnomad OTH

AF:

0.145

GnomAD3 exomes

AF:

0.118

AC:

29514

AN:

249976

Hom.:

2124

AF XY:

0.119

AC XY:

16153

AN XY:

135298

show subpopulations

Gnomad AFR exome

AF:

0.189

Gnomad AMR exome

AF:

0.0705

Gnomad ASJ exome

AF:

0.187

Gnomad EAS exome

AF:

0.000163

Gnomad SAS exome

AF:

0.0894

Gnomad FIN exome

AF:

0.0940

Gnomad NFE exome

AF:

0.147

Gnomad OTH exome

AF:

0.129

GnomAD4 exome

AF:

0.137

AC:

200361

AN:

1460616

Hom.:

14825

Cov.:

AF XY:

0.136

AC XY:

98949

AN XY:

726670

show subpopulations

Gnomad4 AFR exome

AF:

0.195

Gnomad4 AMR exome

AF:

0.0762

Gnomad4 ASJ exome

AF:

0.188

Gnomad4 EAS exome

AF:

0.000277

Gnomad4 SAS exome

AF:

0.0901

Gnomad4 FIN exome

AF:

0.0946

Gnomad4 NFE exome

AF:

0.147

Gnomad4 OTH exome

AF:

0.141

GnomAD4 genome

AF:

0.141

AC:

21408

AN:

152274

Hom.:

1641

Cov.:

AF XY:

0.136

AC XY:

10140

AN XY:

74458

show subpopulations

Gnomad4 AFR

AF:

0.183

Gnomad4 AMR

AF:

0.101

Gnomad4 ASJ

AF:

0.186

Gnomad4 EAS

AF:

0.000964

Gnomad4 SAS

AF:

0.0920

Gnomad4 FIN

AF:

0.0930

Gnomad4 NFE

AF:

0.143

Gnomad4 OTH

AF:

0.143

Alfa

AF:

0.140

Hom.:

2994

Bravo

AF:

0.144

Asia WGS

AF:

0.0410

AC:

145

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 13, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Benign

0.91

BranchPoint Hunter

2.0

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00036

dbscSNV1_RF

Benign

0.042

SpliceAI score (max)

0.060

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over