rs2296666
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001393.4(ECM2):c.1170+32T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.321 in 1,510,748 control chromosomes in the GnomAD database, including 83,655 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 0.40 ( 14425 hom., cov: 32)
Exomes 𝑓: 0.31 ( 69230 hom. )
Consequence
ECM2
NM_001393.4 intron
NM_001393.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0670
Genes affected
CENPP (HGNC:32933): (centromere protein P) CENPP is a subunit of a CENPH (MIM 605607)-CENPI (MIM 300065)-associated centromeric complex that targets CENPA (MIM 117139) to centromeres and is required for proper kinetochore function and mitotic progression (Okada et al., 2006 [PubMed 16622420]).[supplied by OMIM, Mar 2008]
ECM2 (HGNC:3154): (extracellular matrix protein 2) ECM2 encodes extracellular matrix protein 2, so named because it shares extensive similarity with known extracelluar matrix proteins. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CENPP | NM_001012267.3 | c.565-99335A>G | intron_variant | ENST00000375587.8 | NP_001012267.1 | |||
ECM2 | NM_001393.4 | c.1170+32T>C | intron_variant | ENST00000344604.10 | NP_001384.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ECM2 | ENST00000344604.10 | c.1170+32T>C | intron_variant | 1 | NM_001393.4 | ENSP00000344758 | P1 | |||
CENPP | ENST00000375587.8 | c.565-99335A>G | intron_variant | 1 | NM_001012267.3 | ENSP00000364737 | P1 | |||
ECM2 | ENST00000444490.6 | c.1104+32T>C | intron_variant | 1 | ENSP00000393971 |
Frequencies
GnomAD3 genomes AF: 0.404 AC: 61375AN: 151994Hom.: 14402 Cov.: 32
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GnomAD3 exomes AF: 0.296 AC: 66890AN: 225822Hom.: 11494 AF XY: 0.293 AC XY: 35829AN XY: 122336
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GnomAD4 exome AF: 0.311 AC: 422829AN: 1358636Hom.: 69230 Cov.: 18 AF XY: 0.309 AC XY: 209800AN XY: 678076
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GnomAD4 genome AF: 0.404 AC: 61439AN: 152112Hom.: 14425 Cov.: 32 AF XY: 0.394 AC XY: 29332AN XY: 74362
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at