chr16-57737425-A-G

Position:

• chr16-57737425-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.40+142A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 905,072 control chromosomes in the GnomAD database, including 8,043 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.13 (1466 hom., cov: 33)
  • Exomes 𝑓: 0.12 (6577 hom.)
• Consequence: KATNB1 NM_005886.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.343

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=-0.83).
• BP6: Variant 16-57737425-A-G is Benign according to our data. Variant chr16-57737425-A-G is described in ClinVar as [Benign]. Clinvar id is 1289490.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KATNB1	NM_005886.3	c.40+142A>G		intron_variant		ENST00000379661.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KATNB1	ENST00000379661.8	c.40+142A>G		intron_variant		5	NM_005886.3	P1

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20240 AN: 152098 Hom.: 1465 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0967

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0923

Gnomad FIN AF: 0.0929

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.139

GnomAD4 exome AF: 0.124 AC: 92988 AN: 752856 Hom.: 6577 AF XY: 0.123 AC XY: 47990 AN XY: 389528

Gnomad4 AFR exome AF: 0.155

Gnomad4 AMR exome AF: 0.0775

Gnomad4 ASJ exome AF: 0.181

Gnomad4 EAS exome AF: 0.000212

Gnomad4 SAS exome AF: 0.0871

Gnomad4 FIN exome AF: 0.0936

Gnomad4 NFE exome AF: 0.136

Gnomad4 OTH exome AF: 0.134

GnomAD4 genome AF: 0.133 AC: 20239 AN: 152216 Hom.: 1466 Cov.: 33 AF XY: 0.128 AC XY: 9553 AN XY: 74434

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.0964

Gnomad4 ASJ AF: 0.185

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0922

Gnomad4 FIN AF: 0.0929

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.137

Alfa AF: 0.136 Hom.: 168

Bravo AF: 0.136

Asia WGS AF: 0.0390 AC: 138 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 13, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.3
DANN	Benign	0.84

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: rs58845971; hg19: chr16-57771337;