Genetic Variant MCEMP1:c.146-188T>G (chr19-7677916-T-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_174918.3(MCEMP1):c.146-188T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000767 in 912,456 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)

Exomes 𝑓: 0.0000077 ( 0 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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MCEMP1	NM_174918.3 link	c.146-188T>G		intron_variant	Intron 2 of 6	ENST00000333598.8	NP_777578.3	Q8IX19A0A384NYE9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
MCEMP1	ENST00000333598.8 link	c.146-188T>G	intron_variant	Intron 2 of 6	1	NM_174918.3	ENSP00000329920.3	Q8IX19
MCEMP1	ENST00000597445.2 link	c.56-188T>G	intron_variant	Intron 1 of 5	3		ENSP00000471413.1	M0R0S5
MCEMP1	ENST00000598851.1 link	n.-13T>G	upstream_gene_variant		3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000767

AC:

AN:

912456

Hom.:

Cov.:

AF XY:

0.00000433

AC XY:

AN XY:

462012

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

21328

American (AMR)

AF:

0.00

AC:

AN:

27838

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

17118

East Asian (EAS)

AF:

0.00

AC:

AN:

36716

South Asian (SAS)

AF:

0.00

AC:

AN:

60376

European-Finnish (FIN)

AF:

0.00

AC:

AN:

44368

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2850

European-Non Finnish (NFE)

AF:

0.0000106

AC:

AN:

660658

Other (OTH)

AF:

0.00

AC:

AN:

41204

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.518

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.4

(source)

DANN

Benign

0.60

PhyloP100

-1.4

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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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19-7677916-T-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over