Variant chr22-30927913-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001303256.3(MORC2):c.3030+106C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 1,373,480 control chromosomes in the GnomAD database, including 81,141 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.38 ( 12131 hom., cov: 33)

Exomes 𝑓: 0.33 ( 69010 hom. )

Consequence

MORC2
NM_001303256.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.904

Variant links:

Genes affected

MORC2 (HGNC:23573): (MORC family CW-type zinc finger 2) This gene encodes a member of the Microrchidia (MORC) protein superfamily. The encoded protein is known to regulate the condensation of heterochromatin in response to DNA damage and play a role in repressing transcription. The protein has been found to regulate the activity of ATP citrate lyase via specific interaction with this enzyme in the cytosol of lipogenic breast cancer cells. The protein also plays a role in lipogenesis and adipocyte differentiation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2016]

MORC2 links:

MORC2-AS1 (HGNC:26662): (MORC2 antisense RNA 1)

MORC2-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 22-30927913-G-C is Benign according to our data. Variant chr22-30927913-G-C is described in ClinVar as [Benign]. Clinvar id is 1245669.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MORC2	NM_001303256.3 linkuse as main transcript	c.3030+106C>G		intron_variant		ENST00000397641.8	NP_001290185.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MORC2	ENST00000397641.8 linkuse as main transcript	c.3030+106C>G		intron_variant		5	NM_001303256.3	ENSP00000380763	P1	Q9Y6X9-1
MORC2-AS1	ENST00000441558.1 linkuse as main transcript	n.68-1964G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes

AF:

0.385

AC:

58482

AN:

152036

Hom.:

12114

Cov.:

show subpopulations

Gnomad AFR

AF:

0.510

Gnomad AMI

AF:

0.295

Gnomad AMR

AF:

0.351

Gnomad ASJ

AF:

0.322

Gnomad EAS

AF:

0.657

Gnomad SAS

AF:

0.298

Gnomad FIN

AF:

0.317

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.317

Gnomad OTH

AF:

0.364

GnomAD4 exome

AF:

0.329

AC:

401633

AN:

1221324

Hom.:

69010

AF XY:

0.326

AC XY:

198805

AN XY:

609196

show subpopulations

Gnomad4 AFR exome

AF:

0.523

Gnomad4 AMR exome

AF:

0.309

Gnomad4 ASJ exome

AF:

0.335

Gnomad4 EAS exome

AF:

0.616

Gnomad4 SAS exome

AF:

0.289

Gnomad4 FIN exome

AF:

0.324

Gnomad4 NFE exome

AF:

0.315

Gnomad4 OTH exome

AF:

0.347

GnomAD4 genome

AF:

0.385

AC:

58540

AN:

152156

Hom.:

12131

Cov.:

AF XY:

0.384

AC XY:

28591

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.511

Gnomad4 AMR

AF:

0.351

Gnomad4 ASJ

AF:

0.322

Gnomad4 EAS

AF:

0.656

Gnomad4 SAS

AF:

0.297

Gnomad4 FIN

AF:

0.317

Gnomad4 NFE

AF:

0.317

Gnomad4 OTH

AF:

0.360

Alfa

AF:

0.355

Hom.:

1221

Bravo

AF:

0.393

Asia WGS

AF:

0.462

AC:

1606

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 06, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

6.3

DANN

Benign

0.60

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