X-38805015-C-T

Variant names:

• chrX-38805015-C-T
• rs185752632
• NM_021242.6:c.69C>T

Variant summary

Our verdict is Benign. The variant received -11 ACMG points: 0P and 11B. BP4_Strong BP6_Moderate BP7 BS2

The NM_021242.6(MID1IP1):​c.69C>T​(p.Gly23Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000243 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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.166
• Publications: 0 publications found

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

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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

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

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.000453 AC: 51 AN: 112590 Hom.: 0 Cov.: 24

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

GnomAD2 exomes AF: 0.000296 AC: 53 AN: 179119 AF XY: 0.000328

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 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.: 0 Cov.: 32 AF XY: 0.000229 AC XY: 82 AN XY: 358571

African (AFR) AF: 0.000876 AC: 23 AN: 26260

American (AMR) AF: 0.000518 AC: 18 AN: 34758

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19169

East Asian (EAS) AF: 0.00 AC: 0 AN: 30044

South Asian (SAS) AF: 0.0000745 AC: 4 AN: 53727

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 40412

Middle Eastern (MID) AF: 0.00170 AC: 7 AN: 4108

European-Non Finnish (NFE) AF: 0.000202 AC: 169 AN: 837798

Other (OTH) AF: 0.000437 AC: 20 AN: 45765

GnomAD4 genome AF: 0.000462 AC: 52 AN: 112641 Hom.: 0 Cov.: 24 AF XY: 0.000661 AC XY: 23 AN XY: 34801

African (AFR) AF: 0.000516 AC: 16 AN: 31031

American (AMR) AF: 0.000834 AC: 9 AN: 10794

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2659

East Asian (EAS) AF: 0.00 AC: 0 AN: 3514

South Asian (SAS) AF: 0.000366 AC: 1 AN: 2731

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6185

Middle Eastern (MID) AF: 0.00461 AC: 1 AN: 217

European-Non Finnish (NFE) AF: 0.000432 AC: 23 AN: 53293

Other (OTH) AF: 0.00131 AC: 2 AN: 1532

Alfa AF: 0.000254 Hom.: 1

Bravo AF: 0.000442

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	8.3
DANN	Benign	0.93
PhyloP100		-0.17
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Mutation Taster		=97/3	polymorphism

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

Other links and lift over

dbSNP: rs185752632; hg19: chrX-38664268;