Genetic Variant MCEMP1:c.146-188T>C (chr19-7677916-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_174918.3(MCEMP1):c.146-188T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 1,063,002 control chromosomes in the GnomAD database, including 173,944 homozygotes. 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 0.50 ( 20108 hom., cov: 31)

Exomes 𝑓: 0.58 ( 153836 hom. )

Consequence

MCEMP1
NM_174918.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.37

Publications

29 publications found

Variant links:

Genes affected

MCEMP1 (HGNC:27291): (mast cell expressed membrane protein 1) This gene encodes a single-pass transmembrane protein. Based on its expression pattern, it is speculated to be involved in regulating mast cell differentiation or immune responses. [provided by RefSeq, Jul 2008]

MCEMP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.745 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174918.3. 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
	MCEMP1	NM_174918.3	MANE Select	c.146-188T>C		intron	N/A	NP_777578.3	Q8IX19-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MCEMP1	ENST00000333598.8	TSL:1 MANE Select	c.146-188T>C	intron	N/A	ENSP00000329920.3	Q8IX19-2
MCEMP1	ENST00000597445.2	TSL:3	c.56-188T>C	intron	N/A	ENSP00000471413.1	M0R0S5
MCEMP1	ENST00000950369.1		c.146-188T>C	intron	N/A	ENSP00000620428.1

Frequencies

GnomAD3 genomes

AF:

0.496

AC:

75269

AN:

151890

Hom.:

20097

Cov.:

show subpopulations

Gnomad AFR

AF:

0.291

Gnomad AMI

AF:

0.410

Gnomad AMR

AF:

0.466

Gnomad ASJ

AF:

0.600

Gnomad EAS

AF:

0.574

Gnomad SAS

AF:

0.766

Gnomad FIN

AF:

0.665

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.569

Gnomad OTH

AF:

0.534

GnomAD4 exome

AF:

0.576

AC:

524808

AN:

910992

Hom.:

153836

Cov.:

AF XY:

0.583

AC XY:

269134

AN XY:

461318

show subpopulations

African (AFR)

AF:

0.289

AC:

6157

AN:

21310

American (AMR)

AF:

0.442

AC:

12307

AN:

27814

Ashkenazi Jewish (ASJ)

AF:

0.591

AC:

10116

AN:

17112

East Asian (EAS)

AF:

0.549

AC:

20144

AN:

36704

South Asian (SAS)

AF:

0.750

AC:

45236

AN:

60350

European-Finnish (FIN)

AF:

0.653

AC:

28968

AN:

44338

Middle Eastern (MID)

AF:

0.688

AC:

1959

AN:

2848

European-Non Finnish (NFE)

AF:

0.571

AC:

376278

AN:

659362

Other (OTH)

AF:

0.575

AC:

23643

AN:

41154

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

11397

22794

34192

45589

56986

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8646

17292

25938

34584

43230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.495

AC:

75314

AN:

152010

Hom.:

20108

Cov.:

AF XY:

0.504

AC XY:

37411

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.291

AC:

12069

AN:

41472

American (AMR)

AF:

0.466

AC:

7101

AN:

15234

Ashkenazi Jewish (ASJ)

AF:

0.600

AC:

2081

AN:

3468

East Asian (EAS)

AF:

0.574

AC:

2970

AN:

5170

South Asian (SAS)

AF:

0.766

AC:

3690

AN:

4818

European-Finnish (FIN)

AF:

0.665

AC:

7037

AN:

10580

Middle Eastern (MID)

AF:

0.663

AC:

195

AN:

294

European-Non Finnish (NFE)

AF:

0.569

AC:

38677

AN:

67958

Other (OTH)

AF:

0.532

AC:

1120

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1844

3688

5533

7377

9221

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

688

1376

2064

2752

3440

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.533

Hom.:

30310

Bravo

AF:

0.468

Asia WGS

AF:

0.662

AC:

2302

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.6

(source)

DANN

Benign

0.58

PhyloP100

-1.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over