Variant X-38805491-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_021242.6(MID1IP1):c.545G>A(p.Gly182Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00349 in 1,204,749 control chromosomes in the GnomAD database, including 9 homozygotes. There are 1,329 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0031 ( 0 hom., 78 hem., cov: 21)

Exomes 𝑓: 0.0035 ( 9 hom. 1251 hem. )

Consequence

MID1IP1
NM_021242.6 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.06

Variant links:

Genes affected

MID1IP1 (HGNC:20715): (MID1 interacting protein 1) Predicted to enable identical protein binding activity and protein C-terminus binding activity. Predicted to be involved in several processes, including negative regulation of microtubule depolymerization; positive regulation of fatty acid biosynthetic process; and protein polymerization. Predicted to be located in cytoplasm and microtubule cytoskeleton. Predicted to be active in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

MID1IP1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.007916033).

BP6

Variant X-38805491-G-A is Benign according to our data. Variant chrX-38805491-G-A is described in ClinVar as [Benign]. Clinvar id is 711083.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Hemizygotes in GnomAd4 at 78 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
MID1IP1	NM_021242.6 linkuse as main transcript	c.545G>A	p.Gly182Asp	missense_variant	3/3	ENST00000614558.3
MID1IP1	NM_001098790.2 linkuse as main transcript	c.545G>A	p.Gly182Asp	missense_variant	3/3
MID1IP1	NM_001098791.2 linkuse as main transcript	c.545G>A	p.Gly182Asp	missense_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
MID1IP1	ENST00000614558.3 linkuse as main transcript	c.545G>A	p.Gly182Asp	missense_variant	3/3	5	NM_021242.6	P1
MID1IP1	ENST00000336949.7 linkuse as main transcript	c.545G>A	p.Gly182Asp	missense_variant	2/2	1		P1
MID1IP1	ENST00000378474.3 linkuse as main transcript	c.545G>A	p.Gly182Asp	missense_variant	3/3	1		P1
MID1IP1	ENST00000457894.5 linkuse as main transcript	c.545G>A	p.Gly182Asp	missense_variant	2/2	3		P1

Frequencies

GnomAD3 genomes

AF:

0.00311

AC:

336

AN:

108120

Hom.:

Cov.:

AF XY:

0.00256

AC XY:

AN XY:

30492

show subpopulations

Gnomad AFR

AF:

0.000338

Gnomad AMI

AF:

0.00444

Gnomad AMR

AF:

0.00854

Gnomad ASJ

AF:

0.00918

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000195

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00388

Gnomad OTH

AF:

0.00554

GnomAD3 exomes

AF:

0.00284

AC:

512

AN:

180016

Hom.:

AF XY:

0.00291

AC XY:

192

AN XY:

65990

show subpopulations

Gnomad AFR exome

AF:

0.000237

Gnomad AMR exome

AF:

0.00249

Gnomad ASJ exome

AF:

0.0103

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000506

Gnomad NFE exome

AF:

0.00414

Gnomad OTH exome

AF:

0.00584

GnomAD4 exome

AF:

0.00353

AC:

3870

AN:

1096599

Hom.:

Cov.:

AF XY:

0.00346

AC XY:

1251

AN XY:

362071

show subpopulations

Gnomad4 AFR exome

AF:

0.000303

Gnomad4 AMR exome

AF:

0.00327

Gnomad4 ASJ exome

AF:

0.0117

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.000620

Gnomad4 NFE exome

AF:

0.00396

Gnomad4 OTH exome

AF:

0.00354

GnomAD4 genome

AF:

0.00311

AC:

336

AN:

108150

Hom.:

Cov.:

AF XY:

0.00255

AC XY:

AN XY:

30532

show subpopulations

Gnomad4 AFR

AF:

0.000337

Gnomad4 AMR

AF:

0.00853

Gnomad4 ASJ

AF:

0.00918

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.000195

Gnomad4 NFE

AF:

0.00388

Gnomad4 OTH

AF:

0.00547

Alfa

AF:

0.00389

Hom.:

162

Bravo

AF:

0.00408

TwinsUK

AF:

0.00162

AC:

ALSPAC

AF:

0.00381

AC:

ESP6500AA

AF:

0.000522

AC:

ESP6500EA

AF:

0.00372

AC:

ExAC

AF:

0.00280

AC:

340

EpiCase

AF:

0.00278

EpiControl

AF:

0.00488

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

Invitae

Jun 22, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.87

BayesDel_addAF

Benign

-0.098

BayesDel_noAF

Uncertain

0.090

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.13

T;T;T;T

FATHMM_MKL

Benign

0.42

LIST_S2

Benign

0.49

.;T;.;.

M_CAP

Uncertain

0.086

MetaRNN

Benign

0.0079

T;T;T;T

MetaSVM

Uncertain

-0.20

MutationAssessor

Uncertain

2.4

M;M;M;M

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.59

PROVEAN

Uncertain

-2.6

.;D;D;D

REVEL

Uncertain

0.63

Sift

Uncertain

0.0050

.;D;D;D

Sift4G

Pathogenic

0.0

D;D;D;D

Polyphen

1.0

D;D;D;D

Vest4

0.41

MVP

0.74

MPC

1.3

ClinPred

0.043

GERP RS

5.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.63

gMVP

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