rs11882592

Variant names:

• chr19-7679089-C-A
• rs11882592
• NM_174918.3:c.509-9C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-7679089-C-A
• chr19-7679089-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_174918.3(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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.16 (2063 hom., cov: 30)
  • Exomes 𝑓: 0.16 (19165 hom.)
• Consequence: MCEMP1 NM_174918.3 intron
• Scores: Splicing: ADA: 0.0001804
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.550
• Publications: 7 publications found

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]

ENSG00000269711 (HGNC:):

ACMG classification

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: NM_174918.3. 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	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.: 30

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

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.: 38 AF XY: 0.155 AC XY: 111947 AN XY: 722196

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

GnomAD4 genome AF: 0.158 AC: 23954 AN: 151972 Hom.: 2063 Cov.: 30 AF XY: 0.157 AC XY: 11668 AN XY: 74262

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: 45 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11086 AN: 67952

Other (OTH) AF: 0.174 AC: 366 AN: 2108

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
DANN	Benign	0.79
PhyloP100		-0.55
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11882592; hg19: chr19-7743975; COSMIC: COSV58040043; COSMIC: COSV58040043;