19-7677916-T-C

Variant names:

• chr19-7677916-T-C
• rs10401670
• NM_174918.3:c.146-188T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.37

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.496 AC: 75269 AN: 151890 Hom.: 20097 Cov.: 31

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.: 12 AF XY: 0.583 AC XY: 269134 AN XY: 461318

Gnomad4 AFR exome AF: 0.289

Gnomad4 AMR exome AF: 0.442

Gnomad4 ASJ exome AF: 0.591

Gnomad4 EAS exome AF: 0.549

Gnomad4 SAS exome AF: 0.750

Gnomad4 FIN exome AF: 0.653

Gnomad4 NFE exome AF: 0.571

Gnomad4 OTH exome AF: 0.575

GnomAD4 genome AF: 0.495 AC: 75314 AN: 152010 Hom.: 20108 Cov.: 31 AF XY: 0.504 AC XY: 37411 AN XY: 74290

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.600

Gnomad4 EAS AF: 0.574

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.532

Alfa AF: 0.543 Hom.: 20683

Bravo AF: 0.468

Asia WGS AF: 0.662 AC: 2302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.58

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

LitVar

Other links and lift over

dbSNP: rs10401670; hg19: chr19-7742802;