Variant rs13081418 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_015175.3(NBEAL2):c.6801+21A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 1,612,402 control chromosomes in the GnomAD database, including 83,948 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.25 ( 5692 hom., cov: 33)

Exomes 𝑓: 0.32 ( 78256 hom. )

Consequence

NBEAL2
NM_015175.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.287

Variant links:

Genes affected

NBEAL2 (HGNC:31928): (neurobeachin like 2) The protein encoded by this gene contains a beige and Chediak-Higashi (BEACH) domain and multiple WD40 domains, and may play a role in megakaryocyte alpha-granule biogenesis. Mutations in this gene are a cause of gray platelet syndrome. [provided by RefSeq, Dec 2011]

NBEAL2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 3-47005868-A-C is Benign according to our data. Variant chr3-47005868-A-C is described in ClinVar as [Benign]. Clinvar id is 260590.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NBEAL2	NM_015175.3 linkuse as main transcript	c.6801+21A>C		intron_variant		ENST00000450053.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NBEAL2	ENST00000450053.8 linkuse as main transcript	c.6801+21A>C		intron_variant		2	NM_015175.3	P2	Q6ZNJ1-1

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

37661

AN:

152088

Hom.:

5692

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0727

Gnomad AMI

AF:

0.249

Gnomad AMR

AF:

0.242

Gnomad ASJ

AF:

0.286

Gnomad EAS

AF:

0.270

Gnomad SAS

AF:

0.351

Gnomad FIN

AF:

0.324

Gnomad MID

AF:

0.253

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.241

GnomAD3 exomes

AF:

0.300

AC:

74537

AN:

248668

Hom.:

11685

AF XY:

0.307

AC XY:

41415

AN XY:

135010

show subpopulations

Gnomad AFR exome

AF:

0.0703

Gnomad AMR exome

AF:

0.262

Gnomad ASJ exome

AF:

0.286

Gnomad EAS exome

AF:

0.257

Gnomad SAS exome

AF:

0.349

Gnomad FIN exome

AF:

0.328

Gnomad NFE exome

AF:

0.332

Gnomad OTH exome

AF:

0.307

GnomAD4 exome

AF:

0.324

AC:

472864

AN:

1460194

Hom.:

78256

Cov.:

AF XY:

0.325

AC XY:

236038

AN XY:

726316

show subpopulations

Gnomad4 AFR exome

AF:

0.0596

Gnomad4 AMR exome

AF:

0.255

Gnomad4 ASJ exome

AF:

0.288

Gnomad4 EAS exome

AF:

0.283

Gnomad4 SAS exome

AF:

0.347

Gnomad4 FIN exome

AF:

0.320

Gnomad4 NFE exome

AF:

0.337

Gnomad4 OTH exome

AF:

0.307

GnomAD4 genome

AF:

0.247

AC:

37657

AN:

152208

Hom.:

5692

Cov.:

AF XY:

0.247

AC XY:

18371

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.0725

Gnomad4 AMR

AF:

0.242

Gnomad4 ASJ

AF:

0.286

Gnomad4 EAS

AF:

0.270

Gnomad4 SAS

AF:

0.352

Gnomad4 FIN

AF:

0.324

Gnomad4 NFE

AF:

0.333

Gnomad4 OTH

AF:

0.237

Alfa

AF:

0.297

Hom.:

1907

Bravo

AF:

0.231

Asia WGS

AF:

0.300

AC:

1040

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Gray platelet syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.80

DANN

Benign

0.51

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