Variant chr3-155160369-GA-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_007289.4(MME):c.1602-20del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 1,559,770 control chromosomes in the GnomAD database, including 58,122 homozygotes. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5208 hom., cov: 22)

Exomes 𝑓: 0.27 ( 52914 hom. )

Consequence

MME
NM_007289.4 intron

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: 0.613

Variant links:

Genes affected

MME (HGNC:7154): (membrane metalloendopeptidase) The protein encoded by this gene is a type II transmembrane glycoprotein and a common acute lymphocytic leukemia antigen that is an important cell surface marker in the diagnosis of human acute lymphocytic leukemia (ALL). The encoded protein is present on leukemic cells of pre-B phenotype, which represent 85% of cases of ALL. This protein is not restricted to leukemic cells, however, and is found on a variety of normal tissues. The protein is a neutral endopeptidase that cleaves peptides at the amino side of hydrophobic residues and inactivates several peptide hormones including glucagon, enkephalins, substance P, neurotensin, oxytocin, and bradykinin. [provided by RefSeq, Aug 2017]

MME links:

MME-AS1 (HGNC:40376): (MME antisense RNA 1)

MME-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 3-155160369-GA-G is Benign according to our data. Variant chr3-155160369-GA-G is described in ClinVar as [Benign]. Clinvar id is 1240795.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-155160369-GA-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MME	NM_007289.4 linkuse as main transcript	c.1602-20del		intron_variant		ENST00000360490.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MME	ENST00000360490.7 linkuse as main transcript	c.1602-20del		intron_variant		1	NM_007289.4	P1
MME-AS1	ENST00000484721.2 linkuse as main transcript	n.215-1387del		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.257

AC:

39008

AN:

151780

Hom.:

5203

Cov.:

show subpopulations

Gnomad AFR

AF:

0.277

Gnomad AMI

AF:

0.479

Gnomad AMR

AF:

0.195

Gnomad ASJ

AF:

0.290

Gnomad EAS

AF:

0.0778

Gnomad SAS

AF:

0.189

Gnomad FIN

AF:

0.184

Gnomad MID

AF:

0.306

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.261

GnomAD3 exomes

AF:

0.229

AC:

57370

AN:

250728

Hom.:

7367

AF XY:

0.232

AC XY:

31418

AN XY:

135522

show subpopulations

Gnomad AFR exome

AF:

0.281

Gnomad AMR exome

AF:

0.140

Gnomad ASJ exome

AF:

0.297

Gnomad EAS exome

AF:

0.0773

Gnomad SAS exome

AF:

0.185

Gnomad FIN exome

AF:

0.186

Gnomad NFE exome

AF:

0.286

Gnomad OTH exome

AF:

0.249

GnomAD4 exome

AF:

0.267

AC:

375999

AN:

1407872

Hom.:

52914

Cov.:

AF XY:

0.265

AC XY:

186658

AN XY:

703834

show subpopulations

Gnomad4 AFR exome

AF:

0.275

Gnomad4 AMR exome

AF:

0.147

Gnomad4 ASJ exome

AF:

0.298

Gnomad4 EAS exome

AF:

0.0846

Gnomad4 SAS exome

AF:

0.182

Gnomad4 FIN exome

AF:

0.193

Gnomad4 NFE exome

AF:

0.289

Gnomad4 OTH exome

AF:

0.261

GnomAD4 genome

AF:

0.257

AC:

39026

AN:

151898

Hom.:

5208

Cov.:

AF XY:

0.249

AC XY:

18471

AN XY:

74244

show subpopulations

Gnomad4 AFR

AF:

0.277

Gnomad4 AMR

AF:

0.195

Gnomad4 ASJ

AF:

0.290

Gnomad4 EAS

AF:

0.0780

Gnomad4 SAS

AF:

0.189

Gnomad4 FIN

AF:

0.184

Gnomad4 NFE

AF:

0.283

Gnomad4 OTH

AF:

0.259

Alfa

AF:

0.184

Hom.:

533

Bravo

AF:

0.260

Asia WGS

AF:

0.148

AC:

516

AN:

3478

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	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 05, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.090

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