Variant X-38805015-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_021242.6(MID1IP1):c.69C>T(p.Gly23=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000243 in 1,204,682 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 105 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00046 ( 0 hom., 23 hem., cov: 24)

Exomes 𝑓: 0.00022 ( 0 hom. 82 hem. )

Consequence

MID1IP1
NM_021242.6 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.166

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 -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.48).

BP6

Variant X-38805015-C-T is Benign according to our data. Variant chrX-38805015-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2660301.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.166 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 23 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
MID1IP1	NM_021242.6 linkuse as main transcript	c.69C>T	p.Gly23=	synonymous_variant	3/3	ENST00000614558.3
MID1IP1	NM_001098790.2 linkuse as main transcript	c.69C>T	p.Gly23=	synonymous_variant	3/3
MID1IP1	NM_001098791.2 linkuse as main transcript	c.69C>T	p.Gly23=	synonymous_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris
MID1IP1	ENST00000614558.3 linkuse as main transcript	c.69C>T	p.Gly23=	synonymous_variant	3/3	5	NM_021242.6	P1
MID1IP1	ENST00000336949.7 linkuse as main transcript	c.69C>T	p.Gly23=	synonymous_variant	2/2	1		P1
MID1IP1	ENST00000378474.3 linkuse as main transcript	c.69C>T	p.Gly23=	synonymous_variant	3/3	1		P1
MID1IP1	ENST00000457894.5 linkuse as main transcript	c.69C>T	p.Gly23=	synonymous_variant	2/2	3		P1

Frequencies

GnomAD3 genomes

AF:

0.000453

AC:

AN:

112590

Hom.:

Cov.:

AF XY:

0.000662

AC XY:

AN XY:

34740

show subpopulations

Gnomad AFR

AF:

0.000517

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000835

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00420

Gnomad NFE

AF:

0.000432

Gnomad OTH

AF:

0.00132

GnomAD3 exomes

AF:

0.000296

AC:

AN:

179119

Hom.:

AF XY:

0.000328

AC XY:

AN XY:

64011

show subpopulations

Gnomad AFR exome

AF:

0.000306

Gnomad AMR exome

AF:

0.000600

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000163

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000375

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000221

AC:

241

AN:

1092041

Hom.:

Cov.:

AF XY:

0.000229

AC XY:

AN XY:

358571

show subpopulations

Gnomad4 AFR exome

AF:

0.000876

Gnomad4 AMR exome

AF:

0.000518

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000745

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000202

Gnomad4 OTH exome

AF:

0.000437

GnomAD4 genome

AF:

0.000462

AC:

AN:

112641

Hom.:

Cov.:

AF XY:

0.000661

AC XY:

AN XY:

34801

show subpopulations

Gnomad4 AFR

AF:

0.000516

Gnomad4 AMR

AF:

0.000834

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000366

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000432

Gnomad4 OTH

AF:

0.00131

Alfa

AF:

0.000254

Hom.:

Bravo

AF:

0.000442

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2022

MID1IP1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Benign

8.3

DANN

Benign

0.93

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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