chrX-135970904-G-C

Position:

• chrX-135970904-G-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_Strong BP6_Moderate

The NM_173470.3(MMGT1):​c.132+154C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.80 (24897 hom., 25251 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: MMGT1 NM_173470.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.349

Genes affected

MMGT1 (HGNC:28100): (membrane magnesium transporter 1) Contributes to membrane insertase activity. Involved in protein insertion into ER membrane by stop-transfer membrane-anchor sequence and tail-anchored membrane protein insertion into ER membrane. Is integral component of endoplasmic reticulum membrane. Part of EMC complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant X-135970904-G-C is Benign according to our data. Variant chrX-135970904-G-C is described in ClinVar as [Benign]. Clinvar id is 1249185.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MMGT1	NM_173470.3	c.132+154C>G		intron_variant		ENST00000305963.3
MMGT1	NM_001330000.2	c.132+154C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MMGT1	ENST00000305963.3	c.132+154C>G		intron_variant		1	NM_173470.3	P1
MMGT1	ENST00000679621.1	c.132+154C>G		intron_variant				P1
MMGT1	ENST00000680510.2	c.79+2693C>G		intron_variant
MMGT1	ENST00000681201.1	c.132+154C>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.798 AC: 87287 AN: 109418 Hom.: 24910 Cov.: 22 AF XY: 0.795 AC XY: 25220 AN XY: 31726

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.721

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.863

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.824

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.797 AC: 87296 AN: 109467 Hom.: 24897 Cov.: 22 AF XY: 0.794 AC XY: 25251 AN XY: 31785

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.804

Gnomad4 ASJ AF: 0.863

Gnomad4 EAS AF: 0.867

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.812

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.825

Alfa AF: 0.682 Hom.: 2581

Bravo AF: 0.790

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.35
DANN	Benign	0.61

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs4478733; hg19: chrX-135053063;