rs745982845

Variant names:

• chrX-38805142-C-A
• rs745982845
• NM_021242.6:c.196C>A

Your query was ambiguous. Multiple possible variants found:

• chrX-38805142-C-A
• chrX-38805142-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_021242.6(MID1IP1):​c.196C>A​(p.Arg66Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R66C) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 23)
• Consequence: MID1IP1 NM_021242.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 1 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.1036464).

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.196C>A	p.Arg66Ser	missense	Exon 3 of 3	NP_067065.1	Q9NPA3
	MID1IP1	NM_001098790.2		c.196C>A	p.Arg66Ser	missense	Exon 3 of 3	NP_001092260.1	Q9NPA3
	MID1IP1	NM_001098791.2		c.196C>A	p.Arg66Ser	missense	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.196C>A	p.Arg66Ser	missense	Exon 3 of 3	ENSP00000483547.1	Q9NPA3
	MID1IP1	ENST00000336949.7	TSL:1	c.196C>A	p.Arg66Ser	missense	Exon 2 of 2	ENSP00000338706.6	Q9NPA3
	MID1IP1	ENST00000378474.3	TSL:1	c.196C>A	p.Arg66Ser	missense	Exon 3 of 3	ENSP00000367735.3	Q9NPA3

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 23

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	19
DANN	Benign	0.96
DEOGEN2	Benign	0.010	T
FATHMM_MKL	Benign	0.17	N
LIST_S2	Benign	0.39	T
M_CAP	Benign	0.024	T
MetaRNN	Benign	0.10	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.41	N
PhyloP100		-0.0090
PrimateAI	Uncertain	0.53	T
PROVEAN	Benign	0.19	N
REVEL	Benign	0.22
Sift	Benign	0.35	T
Sift4G	Benign	0.69	T
Polyphen		0.012	B
Vest4		0.36
MutPred		0.54		Gain of glycosylation at R66 (P = 0.0038)
MVP		0.46
MPC		0.39
ClinPred		0.043	T
GERP RS		0.12
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3
Varity_R		0.23
gMVP		0.65
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: rs745982845; hg19: chrX-38664395;