Variant X-101237784-G-A 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_001939.3(DRP2):c.438+9G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0923 in 1,121,122 control chromosomes in the GnomAD database, including 3,521 homozygotes. There are 31,929 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 449 hom., 3089 hem., cov: 22)

Exomes 𝑓: 0.091 ( 3072 hom. 28840 hem. )

Consequence

DRP2
NM_001939.3 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.580

Variant links:

Genes affected

DRP2 (HGNC:3032): (dystrophin related protein 2) Members of the dystrophin family of proteins perform a critical role in the maintenance of membrane-associated complexes at points of intercellular contact in vertebrate cells. The protein encoded by this gene is predicted to resemble certain short C-terminal isoforms of dystrophin and dystrophin-related protein 1 (DRP1 or utrophin). DRP2 is expressed principally in the brain and spinal cord. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]

DRP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP6

Variant X-101237784-G-A is Benign according to our data. Variant chrX-101237784-G-A is described in ClinVar as [Benign]. Clinvar id is 1273592.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-101237784-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.132 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
DRP2	NM_001939.3 linkuse as main transcript	c.438+9G>A	intron_variant	ENST00000395209.8
DRP2	NM_001171184.2 linkuse as main transcript	c.204+9G>A	intron_variant
DRP2	XM_017029333.2 linkuse as main transcript	c.438+9G>A	intron_variant
DRP2	XM_047441894.1 linkuse as main transcript	c.438+9G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DRP2	ENST00000395209.8 linkuse as main transcript	c.438+9G>A		intron_variant		1	NM_001939.3	P1	Q13474-1

Frequencies

GnomAD3 genomes

AF:

0.0999

AC:

11119

AN:

111277

Hom.:

447

Cov.:

AF XY:

0.0919

AC XY:

3078

AN XY:

33495

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.272

Gnomad AMR

AF:

0.0568

Gnomad ASJ

AF:

0.0957

Gnomad EAS

AF:

0.00225

Gnomad SAS

AF:

0.0885

Gnomad FIN

AF:

0.0501

Gnomad MID

AF:

0.119

Gnomad NFE

AF:

0.0991

Gnomad OTH

AF:

0.103

GnomAD3 exomes

AF:

0.0810

AC:

11859

AN:

146494

Hom.:

458

AF XY:

0.0859

AC XY:

3499

AN XY:

40726

show subpopulations

Gnomad AFR exome

AF:

0.145

Gnomad AMR exome

AF:

0.0330

Gnomad ASJ exome

AF:

0.103

Gnomad EAS exome

AF:

0.000522

Gnomad SAS exome

AF:

0.0870

Gnomad FIN exome

AF:

0.0602

Gnomad NFE exome

AF:

0.0989

Gnomad OTH exome

AF:

0.0871

GnomAD4 exome

AF:

0.0914

AC:

92300

AN:

1009789

Hom.:

3072

Cov.:

AF XY:

0.0933

AC XY:

28840

AN XY:

309097

show subpopulations

Gnomad4 AFR exome

AF:

0.147

Gnomad4 AMR exome

AF:

0.0396

Gnomad4 ASJ exome

AF:

0.0946

Gnomad4 EAS exome

AF:

0.000388

Gnomad4 SAS exome

AF:

0.0972

Gnomad4 FIN exome

AF:

0.0606

Gnomad4 NFE exome

AF:

0.0959

Gnomad4 OTH exome

AF:

0.0916

GnomAD4 genome

AF:

0.100

AC:

11134

AN:

111333

Hom.:

449

Cov.:

AF XY:

0.0920

AC XY:

3089

AN XY:

33561

show subpopulations

Gnomad4 AFR

AF:

0.135

Gnomad4 AMR

AF:

0.0567

Gnomad4 ASJ

AF:

0.0957

Gnomad4 EAS

AF:

0.00226

Gnomad4 SAS

AF:

0.0876

Gnomad4 FIN

AF:

0.0501

Gnomad4 NFE

AF:

0.0991

Gnomad4 OTH

AF:

0.101

Alfa

AF:

0.0899

Hom.:

1830

Bravo

AF:

0.104

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 11, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

DANN

Benign

0.74

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