16-57741460-A-G

Position:

• chr16-57741460-A-G

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.41-227A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.968 in 152,348 control chromosomes in the GnomAD database, including 71,567 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.97 (71567 hom., cov: 34)
• Consequence: KATNB1 NM_005886.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.17

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=-1.0).
• BP6: Variant 16-57741460-A-G is Benign according to our data. Variant chr16-57741460-A-G is described in ClinVar as [Benign]. Clinvar id is 1226938.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.984 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KATNB1	NM_005886.3	c.41-227A>G		intron_variant		ENST00000379661.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KATNB1	ENST00000379661.8	c.41-227A>G		intron_variant		5	NM_005886.3	P1

Frequencies

GnomAD3 genomes AF: 0.968 AC: 147285 AN: 152230 Hom.: 71502 Cov.: 34

Gnomad AFR AF: 0.992

Gnomad AMI AF: 0.998

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.992

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.963

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.958

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

GnomAD4 genome AF: 0.968 AC: 147412 AN: 152348 Hom.: 71567 Cov.: 34 AF XY: 0.965 AC XY: 71891 AN XY: 74486

Gnomad4 AFR AF: 0.992

Gnomad4 AMR AF: 0.925

Gnomad4 ASJ AF: 0.992

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.964

Gnomad4 FIN AF: 0.965

Gnomad4 NFE AF: 0.982

Gnomad4 OTH AF: 0.958

Alfa AF: 0.978 Hom.: 9035

Bravo AF: 0.961

Asia WGS AF: 0.846 AC: 2945 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 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.98
DANN	Benign	0.31

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: rs2967150; hg19: chr16-57775372;