rs10401670

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr19-7677916-T-A
• chr19-7677916-T-C
• chr19-7677916-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_174918.3(MCEMP1):​c.146-188T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: 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=-0.83).

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 912454 Hom.: 0 Cov.: 12 AF XY: 0.00 AC XY: 0 AN XY: 462010

African (AFR) AF: 0.00 AC: 0 AN: 21328

American (AMR) AF: 0.00 AC: 0 AN: 27838

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17118

East Asian (EAS) AF: 0.00 AC: 0 AN: 36716

South Asian (SAS) AF: 0.00 AC: 0 AN: 60376

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44368

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2850

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 660656

Other (OTH) AF: 0.00 AC: 0 AN: 41204

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 30310

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.73
PhyloP100		-1.4

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;