Variant 18-47028776-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6

The NM_001387690.1(KATNAL2):c.52-17681T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.32 ( 48 hom., cov: 15)

Exomes 𝑓: 0.37 ( 417 hom. )

Failed GnomAD Quality Control

Consequence

KATNAL2
NM_001387690.1 intron

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.00200

Variant links:

Genes affected

KATNAL2 (HGNC:25387): (katanin catalytic subunit A1 like 2) Predicted to enable microtubule-severing ATPase activity. Predicted to be involved in cytoplasmic microtubule organization. Located in cytoplasm; microtubule; and spindle pole. [provided by Alliance of Genome Resources, Apr 2022]

KATNAL2 links:

ELOA3P (HGNC:24617): (elongin A3, pseudogene) The SIII (or elongin) transcription elongation factor complex stimulates the rate of transcription elongation by RNA polymerase II by suppressing the transient pausing of the polymerase at many sites along the DNA template. This gene represents a likely pseudogene of ELOA (GeneID: 6924). [provided by RefSeq, Jun 2020]

ELOA3P links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0020078123).

BP6

Variant 18-47028776-T-G is Benign according to our data. Variant chr18-47028776-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 3356626.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
KATNAL2	NM_001387690.1 linkuse as main transcript	c.52-17681T>G		intron_variant		ENST00000683218.1	NP_001374619.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
KATNAL2	ENST00000683218.1 linkuse as main transcript	c.52-17681T>G		intron_variant			NM_001387690.1	ENSP00000508137	P1	Q8IYT4-1
ELOA3P	ENST00000674825.1 linkuse as main transcript	n.1067A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

25354

AN:

79238

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0930

Gnomad AMI

AF:

0.479

Gnomad AMR

AF:

0.379

Gnomad ASJ

AF:

0.391

Gnomad EAS

AF:

0.296

Gnomad SAS

AF:

0.376

Gnomad FIN

AF:

0.448

Gnomad MID

AF:

0.366

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.379

GnomAD3 exomes

AF:

0.144

AC:

21398

AN:

149046

Hom.:

AF XY:

0.151

AC XY:

12256

AN XY:

81030

show subpopulations

Gnomad AFR exome

AF:

0.0169

Gnomad AMR exome

AF:

0.129

Gnomad ASJ exome

AF:

0.166

Gnomad EAS exome

AF:

0.0717

Gnomad SAS exome

AF:

0.186

Gnomad FIN exome

AF:

0.122

Gnomad NFE exome

AF:

0.168

Gnomad OTH exome

AF:

0.163

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.367

AC:

316374

AN:

861474

Hom.:

417

Cov.:

AF XY:

0.368

AC XY:

159029

AN XY:

431842

show subpopulations

Gnomad4 AFR exome

AF:

0.0795

Gnomad4 AMR exome

AF:

0.345

Gnomad4 ASJ exome

AF:

0.345

Gnomad4 EAS exome

AF:

0.263

Gnomad4 SAS exome

AF:

0.361

Gnomad4 FIN exome

AF:

0.409

Gnomad4 NFE exome

AF:

0.380

Gnomad4 OTH exome

AF:

0.341

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.320

AC:

25353

AN:

79308

Hom.:

Cov.:

AF XY:

0.323

AC XY:

12344

AN XY:

38202

show subpopulations

Gnomad4 AFR

AF:

0.0929

Gnomad4 AMR

AF:

0.378

Gnomad4 ASJ

AF:

0.391

Gnomad4 EAS

AF:

0.296

Gnomad4 SAS

AF:

0.375

Gnomad4 FIN

AF:

0.448

Gnomad4 NFE

AF:

0.421

Gnomad4 OTH

AF:

0.373

Alfa

AF:

0.133

Hom.:

ESP6500AA

AF:

0.0219

AC:

ESP6500EA

AF:

0.0893

AC:

595

ExAC

AF:

0.189

AC:

20065

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

ELOA3P-related condition

Benign:1

Likely benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 08, 2023

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.095

BayesDel_addAF

Benign

-0.50

BayesDel_noAF

Benign

-0.52

CADD

Benign

7.9

DANN

Benign

0.64

DEOGEN2

Benign

0.036

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.0035

LIST_S2

Benign

0.81

MetaRNN

Benign

0.0020

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.34

MutationTaster

Benign

1.0

N;N;N;N

PrimateAI

Benign

0.42

PROVEAN

Benign

1.5

REVEL

Benign

0.035

Sift

Benign

0.071

Sift4G

Uncertain

0.051

Polyphen

0.0050

Vest4

0.18

ClinPred

0.0020

GERP RS

-1.6

Varity_R

0.042

gMVP

0.94

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

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