chrX-38805421-T-A

Position:

chrX-38805421-T-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_021242.6(MID1IP1):c.475T>A(p.Ser159Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000962 in 1,206,154 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 36 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000083 ( 0 hom., 3 hem., cov: 21)

Exomes 𝑓: 0.000097 ( 0 hom. 33 hem. )

Consequence

MID1IP1
NM_021242.6 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.63

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 Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.2009291).

BS2

High Hemizygotes in GnomAd4 at 3 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MID1IP1	NM_021242.6 linkuse as main transcript	c.475T>A	p.Ser159Thr	missense_variant	3/3	ENST00000614558.3	NP_067065.1	Q9NPA3
MID1IP1	NM_001098790.2 linkuse as main transcript	c.475T>A	p.Ser159Thr	missense_variant	3/3		NP_001092260.1	Q9NPA3
MID1IP1	NM_001098791.2 linkuse as main transcript	c.475T>A	p.Ser159Thr	missense_variant	2/2		NP_001092261.1	Q9NPA3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MID1IP1	ENST00000614558.3 linkuse as main transcript	c.475T>A	p.Ser159Thr	missense_variant	3/3	5	NM_021242.6	ENSP00000483547.1	Q9NPA3
MID1IP1	ENST00000336949.7 linkuse as main transcript	c.475T>A	p.Ser159Thr	missense_variant	2/2	1		ENSP00000338706.6	Q9NPA3
MID1IP1	ENST00000378474.3 linkuse as main transcript	c.475T>A	p.Ser159Thr	missense_variant	3/3	1		ENSP00000367735.3	Q9NPA3
MID1IP1	ENST00000457894.5 linkuse as main transcript	c.475T>A	p.Ser159Thr	missense_variant	2/2	3		ENSP00000416670.1	Q9NPA3

Frequencies

GnomAD3 genomes

AF:

0.0000832

AC:

AN:

108230

Hom.:

Cov.:

AF XY:

0.0000982

AC XY:

AN XY:

30564

show subpopulations

Gnomad AFR

AF:

0.0000675

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000134

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000167

AC:

AN:

179657

Hom.:

AF XY:

0.0000153

AC XY:

AN XY:

65293

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000378

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000975

AC:

107

AN:

1097924

Hom.:

Cov.:

AF XY:

0.0000908

AC XY:

AN XY:

363308

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000118

Gnomad4 OTH exome

AF:

0.000174

GnomAD4 genome

AF:

0.0000832

AC:

AN:

108230

Hom.:

Cov.:

AF XY:

0.0000982

AC XY:

AN XY:

30564

show subpopulations

Gnomad4 AFR

AF:

0.0000675

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000134

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000604

ExAC

AF:

0.0000165

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 25, 2024

The c.475T>A (p.S159T) alteration is located in exon 2 (coding exon 1) of the MID1IP1 gene. This alteration results from a T to A substitution at nucleotide position 475, causing the serine (S) at amino acid position 159 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.22

BayesDel_addAF

Benign

-0.097

BayesDel_noAF

Benign

-0.38

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.029

T;T;T;T

FATHMM_MKL

Uncertain

0.80

LIST_S2

Benign

0.75

.;T;.;.

M_CAP

Benign

0.020

MetaRNN

Benign

0.20

T;T;T;T

MetaSVM

Benign

-0.95

MutationAssessor

Benign

0.81

L;L;L;L

MutationTaster

Benign

0.61

D;D;D

PrimateAI

Uncertain

0.75

PROVEAN

Benign

-1.1

.;N;N;N

REVEL

Benign

0.067

Sift

Uncertain

0.0080

.;D;D;D

Sift4G

Benign

0.45

T;T;T;T

Polyphen

0.31

B;B;B;B

Vest4

0.18

MutPred

0.65

Loss of stability (P = 0.0949);Loss of stability (P = 0.0949);Loss of stability (P = 0.0949);Loss of stability (P = 0.0949);

MVP

0.61

MPC

0.50

ClinPred

0.13

GERP RS

3.8

Varity_R

0.32

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