chr16-57741390-G-A

Position:

• chr16-57741390-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_005886.3(KATNB1):​c.41-297G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.081 in 152,278 control chromosomes in the GnomAD database, including 577 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.081 (577 hom., cov: 33)
• Consequence: KATNB1 NM_005886.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.945

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 16-57741390-G-A is Benign according to our data. Variant chr16-57741390-G-A is described in ClinVar as [Benign]. Clinvar id is 1247108.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KATNB1	NM_005886.3	c.41-297G>A		intron_variant		ENST00000379661.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KATNB1	ENST00000379661.8	c.41-297G>A		intron_variant		5	NM_005886.3	P1

Frequencies

GnomAD3 genomes AF: 0.0810 AC: 12327 AN: 152160 Hom.: 573 Cov.: 33

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0631

Gnomad EAS AF: 0.0523

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.0414

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.0703

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0810 AC: 12341 AN: 152278 Hom.: 577 Cov.: 33 AF XY: 0.0794 AC XY: 5910 AN XY: 74450

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.0469

Gnomad4 ASJ AF: 0.0631

Gnomad4 EAS AF: 0.0524

Gnomad4 SAS AF: 0.120

Gnomad4 FIN AF: 0.0414

Gnomad4 NFE AF: 0.0783

Gnomad4 OTH AF: 0.0696

Alfa AF: 0.0846 Hom.: 82

Bravo AF: 0.0805

Asia WGS AF: 0.0830 AC: 291 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 21, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.21
DANN	Benign	0.76

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

LitVar

Other links and lift over

dbSNP: rs12934225; hg19: chr16-57775302;