Genetic Variant MID1IP1:c.-1815T>C (chrX-38802863-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_021242.6(MID1IP1):c.-1815T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.73 ( 21865 hom., 22884 hem., cov: 22)

Exomes 𝑓: 0.74 ( 14 hom. 60 hem. )

Failed GnomAD Quality Control

Consequence

MID1IP1
NM_021242.6 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.784

Publications

1 publications found

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:

MID1IP1-AS1 (HGNC:40932): (MID1IP1 antisense RNA 1)

MID1IP1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAdExome4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021242.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MID1IP1	NM_021242.6	MANE Select	c.-1815T>C	5_prime_UTR	Exon 2 of 3	NP_067065.1	Q9NPA3
MID1IP1	NM_001098790.2		c.-369+1376T>C	intron	N/A	NP_001092260.1	Q9NPA3
MID1IP1	NM_001098791.2		c.-265+1376T>C	intron	N/A	NP_001092261.1	Q9NPA3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MID1IP1	ENST00000614558.3	TSL:5 MANE Select	c.-1815T>C	5_prime_UTR	Exon 2 of 3	ENSP00000483547.1	Q9NPA3
MID1IP1	ENST00000336949.7	TSL:1	c.-1815T>C	5_prime_UTR	Exon 1 of 2	ENSP00000338706.6	Q9NPA3
MID1IP1	ENST00000378474.3	TSL:1	c.-369+1376T>C	intron	N/A	ENSP00000367735.3	Q9NPA3

Frequencies

GnomAD3 genomes

AF:

0.733

AC:

80330

AN:

109621

Hom.:

21870

Cov.:

show subpopulations

Gnomad AFR

AF:

0.900

Gnomad AMI

AF:

0.748

Gnomad AMR

AF:

0.535

Gnomad ASJ

AF:

0.747

Gnomad EAS

AF:

0.389

Gnomad SAS

AF:

0.621

Gnomad FIN

AF:

0.672

Gnomad MID

AF:

0.748

Gnomad NFE

AF:

0.711

Gnomad OTH

AF:

0.710

GnomAD4 exome

AF:

0.736

AC:

109

AN:

148

Hom.:

Cov.:

AF XY:

0.811

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.724

AC:

AN:

127

Other (OTH)

AF:

0.818

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.523

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.733

AC:

80362

AN:

109675

Hom.:

21865

Cov.:

AF XY:

0.717

AC XY:

22884

AN XY:

31919

show subpopulations

African (AFR)

AF:

0.900

AC:

27052

AN:

30047

American (AMR)

AF:

0.534

AC:

5601

AN:

10481

Ashkenazi Jewish (ASJ)

AF:

0.747

AC:

1964

AN:

2629

East Asian (EAS)

AF:

0.390

AC:

1350

AN:

3459

South Asian (SAS)

AF:

0.621

AC:

1600

AN:

2578

European-Finnish (FIN)

AF:

0.672

AC:

3784

AN:

5629

Middle Eastern (MID)

AF:

0.727

AC:

152

AN:

209

European-Non Finnish (NFE)

AF:

0.711

AC:

37316

AN:

52489

Other (OTH)

AF:

0.702

AC:

1050

AN:

1495

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

731

1461

2192

2922

3653

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

674

1348

2022

2696

3370

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.720

Hom.:

5887

Bravo

AF:

0.730

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.0

(source)

DANN

Benign

0.40

PhyloP100

-0.78

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over