19-7677916-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 29 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]

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000597445.2	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

African (AFR) AF: 0.289 AC: 6157 AN: 21310

American (AMR) AF: 0.442 AC: 12307 AN: 27814

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 10116 AN: 17112

East Asian (EAS) AF: 0.549 AC: 20144 AN: 36704

South Asian (SAS) AF: 0.750 AC: 45236 AN: 60350

European-Finnish (FIN) AF: 0.653 AC: 28968 AN: 44338

Middle Eastern (MID) AF: 0.688 AC: 1959 AN: 2848

European-Non Finnish (NFE) AF: 0.571 AC: 376278 AN: 659362

Other (OTH) AF: 0.575 AC: 23643 AN: 41154

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

African (AFR) AF: 0.291 AC: 12069 AN: 41472

American (AMR) AF: 0.466 AC: 7101 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.600 AC: 2081 AN: 3468

East Asian (EAS) AF: 0.574 AC: 2970 AN: 5170

South Asian (SAS) AF: 0.766 AC: 3690 AN: 4818

European-Finnish (FIN) AF: 0.665 AC: 7037 AN: 10580

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.569 AC: 38677 AN: 67958

Other (OTH) AF: 0.532 AC: 1120 AN: 2104

Alfa AF: 0.533 Hom.: 30310

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
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10401670; hg19: chr19-7742802;