dbSNP rs185752632: MID1IP1:p.Gly23Gly (chrX-38805015-C-A) – ACMG Classification: Likely_benign (-1 pts)

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_021242.6(MID1IP1):c.69C>A(p.Gly23Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000888 in 112,590 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. G23G) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0000089 ( 0 hom., 0 hem., cov: 24)

Exomes 𝑓: 0.0 ( 0 hom. 0 hem. )

Failed GnomAD Quality Control

Consequence

MID1IP1
NM_021242.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.166

Publications

0 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: Likely_benign. The variant received -1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.45).

BP7

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

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	HGVSp	Effect	Exon Rank	Protein	UniProt
MID1IP1	NM_021242.6	MANE Select	c.69C>A	p.Gly23Gly	synonymous	Exon 3 of 3	NP_067065.1	Q9NPA3
MID1IP1	NM_001098790.2		c.69C>A	p.Gly23Gly	synonymous	Exon 3 of 3	NP_001092260.1	Q9NPA3
MID1IP1	NM_001098791.2		c.69C>A	p.Gly23Gly	synonymous	Exon 2 of 2	NP_001092261.1	Q9NPA3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MID1IP1	ENST00000614558.3	TSL:5 MANE Select	c.69C>A	p.Gly23Gly	synonymous	Exon 3 of 3	ENSP00000483547.1	Q9NPA3
MID1IP1	ENST00000336949.7	TSL:1	c.69C>A	p.Gly23Gly	synonymous	Exon 2 of 2	ENSP00000338706.6	Q9NPA3
MID1IP1	ENST00000378474.3	TSL:1	c.69C>A	p.Gly23Gly	synonymous	Exon 3 of 3	ENSP00000367735.3	Q9NPA3

Frequencies

GnomAD3 genomes

AF:

0.00000888

AC:

AN:

112590

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

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:

0.0000188

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1092042

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

358572

African (AFR)

AF:

0.00

AC:

AN:

26260

American (AMR)

AF:

0.00

AC:

AN:

34758

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

19169

East Asian (EAS)

AF:

0.00

AC:

AN:

30044

South Asian (SAS)

AF:

0.00

AC:

AN:

53726

European-Finnish (FIN)

AF:

0.00

AC:

AN:

40412

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4108

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

837800

Other (OTH)

AF:

0.00

AC:

AN:

45765

GnomAD4 genome

AF:

0.00000888

AC:

AN:

112590

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

34740

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

30964

American (AMR)

AF:

0.00

AC:

AN:

10781

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2659

East Asian (EAS)

AF:

0.00

AC:

AN:

3525

South Asian (SAS)

AF:

0.00

AC:

AN:

2740

European-Finnish (FIN)

AF:

0.00

AC:

AN:

6185

Middle Eastern (MID)

AF:

0.00

AC:

AN:

238

European-Non Finnish (NFE)

AF:

0.0000188

AC:

AN:

53300

Other (OTH)

AF:

0.00

AC:

AN:

1513

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.0000727

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.45

CADD

Benign

7.8

(source)

DANN

Benign

0.89

PhyloP100

-0.17

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

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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