chrX-38802863-T-C

Position:

• chrX-38802863-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MID1IP1	NM_021242.6	c.-1815T>C		5_prime_UTR_variant	2/3	ENST00000614558.3
MID1IP1-AS1	NR_046706.1	n.151+870A>G		intron_variant, non_coding_transcript_variant
MID1IP1	NM_001098790.2	c.-369+1376T>C		intron_variant
MID1IP1	NM_001098791.2	c.-265+1376T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MID1IP1	ENST00000614558.3	c.-1815T>C		5_prime_UTR_variant	2/3	5	NM_021242.6	P1
MID1IP1-AS1	ENST00000436893.1	n.151+870A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.733 AC: 80330 AN: 109621 Hom.: 21870 Cov.: 22 AF XY: 0.717 AC XY: 22839 AN XY: 31855

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.: 14 Cov.: 0 AF XY: 0.811 AC XY: 60 AN XY: 74

Gnomad4 AFR exome AF: 1.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 1.00

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.724

Gnomad4 OTH exome AF: 0.818

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.733 AC: 80362 AN: 109675 Hom.: 21865 Cov.: 22 AF XY: 0.717 AC XY: 22884 AN XY: 31919

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.534

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.702

Alfa AF: 0.720 Hom.: 5887

Bravo AF: 0.730

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.40

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

Other links and lift over

dbSNP: rs198782; hg19: chrX-38662116;