7-100430287-C-T

Variant names:

• chr7-100430287-C-T
• rs1159115478
• NM_019606.6:c.269C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_019606.6(MEPCE):​c.269C>T​(p.Pro90Leu) variant causes a missense 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. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P90H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MEPCE NM_019606.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 1 publications found

Genes affected

MEPCE (HGNC:20247): (methylphosphate capping enzyme) Enables 7SK snRNA binding activity and RNA 5'-methyltransferase activity. Involved in RNA modification; positive regulation of protein localization to Cajal body; and positive regulation of snRNA transcription by RNA polymerase II. Located in nucleus. Part of 7SK snRNP. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000289690 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.090016246).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_019606.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEPCE	NM_019606.6	MANE Select	c.269C>T	p.Pro90Leu	missense	Exon 1 of 4	NP_062552.2
	MEPCE	NM_001194990.2		c.-811-328C>T		intron	N/A	NP_001181919.1	Q7L2J0-2
	MEPCE	NM_001194991.2		c.-396-743C>T		intron	N/A	NP_001181920.1	Q7L2J0-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MEPCE	ENST00000310512.4	TSL:1 MANE Select	c.269C>T	p.Pro90Leu	missense	Exon 1 of 4	ENSP00000308546.2	Q7L2J0-1
	ENSG00000289690	ENST00000695707.1		c.-396-743C>T		intron	N/A	ENSP00000512107.1
	MEPCE	ENST00000715739.1		c.269C>T	p.Pro90Leu	missense	Exon 1 of 4	ENSP00000520510.1	Q7L2J0-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.087
BayesDel_addAF	Benign	-0.14	T
BayesDel_noAF	Benign	-0.44
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.016	T
Eigen	Benign	-0.35
Eigen_PC	Benign	-0.15
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Benign	0.64	T
M_CAP	Benign	0.056	D
MetaRNN	Benign	0.090	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.55	N
PhyloP100		1.0
PrimateAI	Uncertain	0.77	T
PROVEAN	Benign	-0.26	N
REVEL	Benign	0.044
Sift	Uncertain	0.0030	D
Sift4G	Benign	0.10	T
Polyphen		0.0	B
Vest4		0.17
MutPred		0.31		Gain of stability (P = 0.0061)
MVP		0.093
MPC		0.99
ClinPred		0.79	D
GERP RS		3.4
PromoterAI		0.066	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2
Varity_R		0.15
gMVP		0.41
Mutation Taster		=73/27	polymorphism

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: rs1159115478; hg19: chr7-100027910;