Variant rs758037994 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2

The NM_012216.4(MID2):c.1074-4del variant causes a splice region, splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.00239 in 1,199,732 control chromosomes in the GnomAD database, including 4 homozygotes. There are 921 hemizygotes in GnomAD. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0018 ( 1 hom., 60 hem., cov: 23)

Exomes 𝑓: 0.0024 ( 3 hom. 861 hem. )

Consequence

MID2
NM_012216.4 splice_region, splice_polypyrimidine_tract, intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 3.64

Variant links:

Genes affected

MID2 (HGNC:7096): (midline 2) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein localizes to microtubular structures in the cytoplasm. Alternate splicing of this gene results in two transcript variants encoding different isoforms. [provided by RefSeq, Feb 2009]

MID2 links:

(HGNC:):

links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP6

Variant X-107915993-CT-C is Benign according to our data. Variant chrX-107915993-CT-C is described in ClinVar as [Likely_benign]. Clinvar id is 445463.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Hemizygotes in GnomAd4 at 60 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MID2	NM_012216.4 linkuse as main transcript	c.1074-4del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000262843.11	NP_036348.2
LOC101928335	NR_110395.1 linkuse as main transcript	n.326+17036del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MID2	ENST00000262843.11 linkuse as main transcript	c.1074-4del		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_012216.4	ENSP00000262843		Q9UJV3-1
	ENST00000663626.2 linkuse as main transcript	n.556+17036del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.00183

AC:

204

AN:

111777

Hom.:

Cov.:

AF XY:

0.00177

AC XY:

AN XY:

33985

show subpopulations

Gnomad AFR

AF:

0.000423

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000850

Gnomad ASJ

AF:

0.000753

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00518

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00281

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.00224

AC:

380

AN:

169336

Hom.:

AF XY:

0.00198

AC XY:

111

AN XY:

56192

show subpopulations

Gnomad AFR exome

AF:

0.000318

Gnomad AMR exome

AF:

0.00155

Gnomad ASJ exome

AF:

0.000571

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00571

Gnomad NFE exome

AF:

0.00311

Gnomad OTH exome

AF:

0.00121

GnomAD4 exome

AF:

0.00245

AC:

2663

AN:

1087904

Hom.:

Cov.:

AF XY:

0.00242

AC XY:

861

AN XY:

355736

show subpopulations

Gnomad4 AFR exome

AF:

0.000272

Gnomad4 AMR exome

AF:

0.00143

Gnomad4 ASJ exome

AF:

0.000680

Gnomad4 EAS exome

AF:

0.0000336

Gnomad4 SAS exome

AF:

0.0000578

Gnomad4 FIN exome

AF:

0.00475

Gnomad4 NFE exome

AF:

0.00273

Gnomad4 OTH exome

AF:

0.00241

GnomAD4 genome

AF:

0.00182

AC:

204

AN:

111828

Hom.:

Cov.:

AF XY:

0.00176

AC XY:

AN XY:

34046

show subpopulations

Gnomad4 AFR

AF:

0.000422

Gnomad4 AMR

AF:

0.000849

Gnomad4 ASJ

AF:

0.000753

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00518

Gnomad4 NFE

AF:

0.00281

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00262

Hom.:

Bravo

AF:

0.00153

Asia WGS

AF:

0.000400

AC:

AN:

2512

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Apr 20, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Sep 24, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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