chr1-150509685-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_004425.4(ECM1):c.146C>A(p.Pro49Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,612,580 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P49P) has been classified as Likely benign.
Frequency
Consequence
NM_004425.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ECM1 | NM_004425.4 | c.146C>A | p.Pro49Gln | missense_variant | 3/10 | ENST00000369047.9 | |
ECM1 | NM_001202858.2 | c.146C>A | p.Pro49Gln | missense_variant | 3/10 | ||
ECM1 | NM_022664.3 | c.146C>A | p.Pro49Gln | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ECM1 | ENST00000369047.9 | c.146C>A | p.Pro49Gln | missense_variant | 3/10 | 1 | NM_004425.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152006Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000513 AC: 129AN: 251440Hom.: 0 AF XY: 0.000390 AC XY: 53AN XY: 135894
GnomAD4 exome AF: 0.000118 AC: 172AN: 1460574Hom.: 0 Cov.: 40 AF XY: 0.000109 AC XY: 79AN XY: 726638
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152006Hom.: 0 Cov.: 31 AF XY: 0.0000943 AC XY: 7AN XY: 74222
ClinVar
Submissions by phenotype
ECM1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 25, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at