Genetic Variant NM_015151.4:c.2079G>A (chr21-46541798-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_015151.4(DIP2A):c.2079G>A(p.Leu693Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 1,613,500 control chromosomes in the GnomAD database, including 90,971 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.37 ( 10961 hom., cov: 32)

Exomes 𝑓: 0.33 ( 80010 hom. )

Consequence

DIP2A
NM_015151.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.0400

Variant links:

Genes affected

DIP2A (HGNC:17217): (disco interacting protein 2 homolog A) The protein encoded by this gene may be involved in axon patterning in the central nervous system. This gene is not highly expressed. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]

DIP2A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.78).

BP6

Variant 21-46541798-G-A is Benign according to our data. Variant chr21-46541798-G-A is described in ClinVar as [Benign]. Clinvar id is 3060508.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.04 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DIP2A	NM_015151.4 link	c.2079G>A	p.Leu693Leu	synonymous_variant	Exon 18 of 38	ENST00000417564.3	NP_055966.2	Q14689-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DIP2A	ENST00000417564.3 link	c.2079G>A	p.Leu693Leu	synonymous_variant	Exon 18 of 38	1	NM_015151.4	ENSP00000392066.2		Q14689-1

Frequencies

GnomAD3 genomes

AF:

0.369

AC:

56034

AN:

151868

Hom.:

10931

Cov.:

show subpopulations

Gnomad AFR

AF:

0.497

Gnomad AMI

AF:

0.417

Gnomad AMR

AF:

0.273

Gnomad ASJ

AF:

0.303

Gnomad EAS

AF:

0.425

Gnomad SAS

AF:

0.329

Gnomad FIN

AF:

0.300

Gnomad MID

AF:

0.421

Gnomad NFE

AF:

0.324

Gnomad OTH

AF:

0.376

GnomAD3 exomes

AF:

0.328

AC:

81753

AN:

249152

Hom.:

14106

AF XY:

0.329

AC XY:

44515

AN XY:

135162

show subpopulations

Gnomad AFR exome

AF:

0.503

Gnomad AMR exome

AF:

0.231

Gnomad ASJ exome

AF:

0.297

Gnomad EAS exome

AF:

0.428

Gnomad SAS exome

AF:

0.319

Gnomad FIN exome

AF:

0.305

Gnomad NFE exome

AF:

0.328

Gnomad OTH exome

AF:

0.326

GnomAD4 exome

AF:

0.328

AC:

478794

AN:

1461514

Hom.:

80010

Cov.:

AF XY:

0.327

AC XY:

238017

AN XY:

727034

show subpopulations

Gnomad4 AFR exome

AF:

0.507

Gnomad4 AMR exome

AF:

0.233

Gnomad4 ASJ exome

AF:

0.295

Gnomad4 EAS exome

AF:

0.438

Gnomad4 SAS exome

AF:

0.320

Gnomad4 FIN exome

AF:

0.308

Gnomad4 NFE exome

AF:

0.323

Gnomad4 OTH exome

AF:

0.341

GnomAD4 genome

AF:

0.369

AC:

56116

AN:

151986

Hom.:

10961

Cov.:

AF XY:

0.364

AC XY:

26997

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.498

Gnomad4 AMR

AF:

0.273

Gnomad4 ASJ

AF:

0.303

Gnomad4 EAS

AF:

0.425

Gnomad4 SAS

AF:

0.330

Gnomad4 FIN

AF:

0.300

Gnomad4 NFE

AF:

0.324

Gnomad4 OTH

AF:

0.379

Alfa

AF:

0.335

Hom.:

7895

Bravo

AF:

0.375

Asia WGS

AF:

0.407

AC:

1417

AN:

3478

EpiCase

AF:

0.319

EpiControl

AF:

0.329

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

DIP2A-related disorder

Benign:1

Oct 18, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as 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

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.95

DANN

Benign

0.48

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