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. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MCEMP1	NM_174918.3	c.509-9C>A		intron_variant	Intron 6 of 6	ENST00000333598.8	NP_777578.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MCEMP1	ENST00000333598.8	c.509-9C>A		intron_variant	Intron 6 of 6	1	NM_174918.3	ENSP00000329920.3
ENSG00000269711	ENST00000597959.1	c.163+106C>A		intron_variant	Intron 2 of 2	4		ENSP00000469811.1
MCEMP1	ENST00000597445.1	c.419-9C>A		intron_variant	Intron 5 of 5	3		ENSP00000471413.1
MCEMP1	ENST00000598851.1	n.*105C>A		downstream_gene_variant		3

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

GnomAD3 exomes AF: 0.164 AC: 39098 AN: 238146 Hom.: 3722 AF XY: 0.156 AC XY: 20113 AN XY: 128636

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 SAS exome AF: 0.0783

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

Gnomad4 AFR exome AF: 0.113

Gnomad4 AMR exome AF: 0.309

Gnomad4 ASJ exome AF: 0.168

Gnomad4 EAS exome AF: 0.0949

Gnomad4 SAS exome AF: 0.0819

Gnomad4 FIN exome AF: 0.173

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.157

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

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0865

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.174

Alfa AF: 0.158 Hom.: 1340

Bravo AF: 0.166

Asia WGS AF: 0.120 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.2
DANN	Benign	0.79

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

LitVar

Other links and lift over

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