Variant X-135973974-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_173470.3(MMGT1):c.-299G>A 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. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.027 ( 33 hom., 294 hem., cov: 12)

Exomes 𝑓: 0.035 ( 430 hom. 10728 hem. )

Consequence

MMGT1
NM_173470.3 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.320

Variant links:

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]

MMGT1 links:

SLC9A6 (HGNC:11079): (solute carrier family 9 member A6) This gene encodes a sodium-hydrogen exchanger that is amember of the solute carrier family 9. The encoded protein localizes to early and recycling endosomes and may be involved in regulating endosomal pH and volume. Defects in this gene are associated with X-linked syndromic cognitive disability, Christianson type. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Apr 2010]

SLC9A6 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

BP6

Variant X-135973974-C-T is Benign according to our data. Variant chrX-135973974-C-T is described in ClinVar as [Benign]. Clinvar id is 1277542.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons	MANE
MMGT1	NM_173470.3 linkuse as main transcript	c.-299G>A	5_prime_UTR_variant	1/4	ENST00000305963.3
MMGT1	NM_001330000.2 linkuse as main transcript	c.-222G>A	5_prime_UTR_variant	1/5
SLC9A6	NM_001400909.1 linkuse as main transcript	c.-241C>T	5_prime_UTR_variant	1/18

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MMGT1	ENST00000305963.3 linkuse as main transcript	c.-299G>A	5_prime_UTR_variant	1/4	1	NM_173470.3	P1	Q8N4V1-1
SLC9A6	ENST00000636347.1 linkuse as main transcript	c.-241C>T	5_prime_UTR_variant	1/18	5		A1	Q92581-3
MMGT1	ENST00000679621.1 linkuse as main transcript	c.-222G>A	5_prime_UTR_variant	1/5			P1	Q8N4V1-1
MMGT1	ENST00000680510.2 linkuse as main transcript	c.-299G>A	5_prime_UTR_variant	1/3

Frequencies

GnomAD3 genomes

AF:

0.0272

AC:

2218

AN:

81519

Hom.:

Cov.:

AF XY:

0.0229

AC XY:

294

AN XY:

12855

show subpopulations

Gnomad AFR

AF:

0.0236

Gnomad AMI

AF:

0.0251

Gnomad AMR

AF:

0.0120

Gnomad ASJ

AF:

0.0233

Gnomad EAS

AF:

0.0534

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.0302

Gnomad MID

AF:

0.0217

Gnomad NFE

AF:

0.0272

Gnomad OTH

AF:

0.0154

GnomAD3 exomes

AF:

0.0350

AC:

3810

AN:

108776

Hom.:

AF XY:

0.0421

AC XY:

1677

AN XY:

39860

show subpopulations

Gnomad AFR exome

AF:

0.0267

Gnomad AMR exome

AF:

0.00750

Gnomad ASJ exome

AF:

0.0228

Gnomad EAS exome

AF:

0.0440

Gnomad SAS exome

AF:

0.102

Gnomad FIN exome

AF:

0.0301

Gnomad NFE exome

AF:

0.0281

Gnomad OTH exome

AF:

0.0297

GnomAD4 exome

AF:

0.0348

AC:

32315

AN:

927335

Hom.:

430

Cov.:

AF XY:

0.0402

AC XY:

10728

AN XY:

266827

show subpopulations

Gnomad4 AFR exome

AF:

0.0264

Gnomad4 AMR exome

AF:

0.00831

Gnomad4 ASJ exome

AF:

0.0251

Gnomad4 EAS exome

AF:

0.0542

Gnomad4 SAS exome

AF:

0.104

Gnomad4 FIN exome

AF:

0.0344

Gnomad4 NFE exome

AF:

0.0314

Gnomad4 OTH exome

AF:

0.0333

GnomAD4 genome

AF:

0.0272

AC:

2218

AN:

81520

Hom.:

Cov.:

AF XY:

0.0228

AC XY:

294

AN XY:

12870

show subpopulations

Gnomad4 AFR

AF:

0.0236

Gnomad4 AMR

AF:

0.0122

Gnomad4 ASJ

AF:

0.0233

Gnomad4 EAS

AF:

0.0533

Gnomad4 SAS

AF:

0.119

Gnomad4 FIN

AF:

0.0302

Gnomad4 NFE

AF:

0.0272

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.0270

Hom.:

1595

Bravo

AF:

0.0259

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 13, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

6.2

DANN

Benign

0.90

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over