Genetic Variant MCEMP1:c.509-9C>A (chr19-7679089-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000333598.8(MCEMP1):c.509-9C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,605,250 control chromosomes in the GnomAD database, including 21,228 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.16 ( 2063 hom., cov: 30)

Exomes 𝑓: 0.16 ( 19165 hom. )

Consequence

MCEMP1
ENST00000333598.8 intron

Scores

Splicing: ADA: 0.0001804

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.550

Publications

7 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:

ENSG00000269711 (HGNC:):

ENSG00000269711 links:

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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=-0.81).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000333598.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MCEMP1	NM_174918.3	MANE Select	c.509-9C>A		intron	N/A	NP_777578.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MCEMP1	ENST00000333598.8	TSL:1 MANE Select	c.509-9C>A	intron	N/A	ENSP00000329920.3
ENSG00000269711	ENST00000597959.1	TSL:4	c.163+106C>A	intron	N/A	ENSP00000469811.1
MCEMP1	ENST00000597445.2	TSL:3	c.419-9C>A	intron	N/A	ENSP00000471413.1

Frequencies

GnomAD3 genomes

AF:

0.158

AC:

23922

AN:

151856

Hom.:

2059

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.184

Gnomad AMR

AF:

0.264

Gnomad ASJ

AF:

0.177

Gnomad EAS

AF:

0.104

Gnomad SAS

AF:

0.0862

Gnomad FIN

AF:

0.172

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.163

Gnomad OTH

AF:

0.171

GnomAD2 exomes

AF:

0.164

AC:

39098

AN:

238146

AF XY:

0.156

show subpopulations

Gnomad AFR exome

AF:

0.113

Gnomad AMR exome

AF:

0.312

Gnomad ASJ exome

AF:

0.172

Gnomad EAS exome

AF:

0.107

Gnomad FIN exome

AF:

0.173

Gnomad NFE exome

AF:

0.156

Gnomad OTH exome

AF:

0.173

GnomAD4 exome

AF:

0.158

AC:

229024

AN:

1453278

Hom.:

19165

Cov.:

AF XY:

0.155

AC XY:

111947

AN XY:

722196

show subpopulations

African (AFR)

AF:

0.113

AC:

3789

AN:

33384

American (AMR)

AF:

0.309

AC:

13412

AN:

43436

Ashkenazi Jewish (ASJ)

AF:

0.168

AC:

4335

AN:

25772

East Asian (EAS)

AF:

0.0949

AC:

3762

AN:

39656

South Asian (SAS)

AF:

0.0819

AC:

6958

AN:

85002

European-Finnish (FIN)

AF:

0.173

AC:

9112

AN:

52818

Middle Eastern (MID)

AF:

0.123

AC:

700

AN:

5694

European-Non Finnish (NFE)

AF:

0.160

AC:

177531

AN:

1107426

Other (OTH)

AF:

0.157

AC:

9425

AN:

60090

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

9778

19557

29335

39114

48892

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6312

12624

18936

25248

31560

<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:

0.158

AC:

23954

AN:

151972

Hom.:

2063

Cov.:

AF XY:

0.157

AC XY:

11668

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.118

AC:

4872

AN:

41434

American (AMR)

AF:

0.264

AC:

4031

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.177

AC:

614

AN:

3472

East Asian (EAS)

AF:

0.104

AC:

536

AN:

5160

South Asian (SAS)

AF:

0.0865

AC:

416

AN:

4812

European-Finnish (FIN)

AF:

0.172

AC:

1821

AN:

10572

Middle Eastern (MID)

AF:

0.153

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.163

AC:

11086

AN:

67952

Other (OTH)

AF:

0.174

AC:

366

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

1011

2022

3034

4045

5056

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

250

500

750

1000

1250

<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:

0.158

Hom.:

2338

Bravo

AF:

0.166

Asia WGS

AF:

0.120

AC:

415

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

3.2

(source)

DANN

Benign

0.79

PhyloP100

-0.55

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00018

dbscSNV1_RF

Benign

0.024

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

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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