Variant 21-46490610-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_015151.4(DIP2A):c.174A>G(p.Pro58Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 1,566,230 control chromosomes in the GnomAD database, including 54,994 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.31 ( 8238 hom., cov: 33)

Exomes 𝑓: 0.25 ( 46756 hom. )

Consequence

DIP2A
NM_015151.4 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.898

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:

DIP2A (HGNC:):

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=-0.93).

BP6

Variant 21-46490610-A-G is Benign according to our data. Variant chr21-46490610-A-G is described in ClinVar as [Benign]. Clinvar id is 3060043.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.898 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DIP2A	NM_015151.4 linkuse as main transcript	c.174A>G	p.Pro58Pro	synonymous_variant	3/38	ENST00000417564.3	NP_055966.2	Q14689-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DIP2A	ENST00000417564.3 linkuse as main transcript	c.174A>G	p.Pro58Pro	synonymous_variant	3/38	1	NM_015151.4	ENSP00000392066.2		Q14689-1

Frequencies

GnomAD3 genomes

AF:

0.314

AC:

47745

AN:

152000

Hom.:

8231

Cov.:

show subpopulations

Gnomad AFR

AF:

0.465

Gnomad AMI

AF:

0.330

Gnomad AMR

AF:

0.237

Gnomad ASJ

AF:

0.265

Gnomad EAS

AF:

0.426

Gnomad SAS

AF:

0.329

Gnomad FIN

AF:

0.268

Gnomad MID

AF:

0.351

Gnomad NFE

AF:

0.239

Gnomad OTH

AF:

0.324

GnomAD3 exomes

AF:

0.273

AC:

48934

AN:

179014

Hom.:

7196

AF XY:

0.276

AC XY:

26260

AN XY:

95234

show subpopulations

Gnomad AFR exome

AF:

0.463

Gnomad AMR exome

AF:

0.199

Gnomad ASJ exome

AF:

0.258

Gnomad EAS exome

AF:

0.425

Gnomad SAS exome

AF:

0.309

Gnomad FIN exome

AF:

0.274

Gnomad NFE exome

AF:

0.239

Gnomad OTH exome

AF:

0.268

GnomAD4 exome

AF:

0.250

AC:

354083

AN:

1414112

Hom.:

46756

Cov.:

AF XY:

0.252

AC XY:

176410

AN XY:

699130

show subpopulations

Gnomad4 AFR exome

AF:

0.481

Gnomad4 AMR exome

AF:

0.200

Gnomad4 ASJ exome

AF:

0.257

Gnomad4 EAS exome

AF:

0.438

Gnomad4 SAS exome

AF:

0.309

Gnomad4 FIN exome

AF:

0.273

Gnomad4 NFE exome

AF:

0.231

Gnomad4 OTH exome

AF:

0.276

GnomAD4 genome

AF:

0.314

AC:

47781

AN:

152118

Hom.:

8238

Cov.:

AF XY:

0.313

AC XY:

23261

AN XY:

74380

show subpopulations

Gnomad4 AFR

AF:

0.464

Gnomad4 AMR

AF:

0.236

Gnomad4 ASJ

AF:

0.265

Gnomad4 EAS

AF:

0.426

Gnomad4 SAS

AF:

0.329

Gnomad4 FIN

AF:

0.268

Gnomad4 NFE

AF:

0.239

Gnomad4 OTH

AF:

0.328

Alfa

AF:

0.259

Hom.:

7143

Bravo

AF:

0.318

Asia WGS

AF:

0.387

AC:

1347

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

DIP2A-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

May 15, 2020

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

-0.93

CADD

Benign

3.3

DANN

Benign

0.41

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