rs13294
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004425.4(ECM1):c.1243G>A(p.Gly415Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.382 in 1,613,130 control chromosomes in the GnomAD database, including 121,478 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004425.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECM1 | NM_004425.4 | c.1243G>A | p.Gly415Ser | missense_variant | 8/10 | ENST00000369047.9 | NP_004416.2 | |
ECM1 | NM_001202858.2 | c.1324G>A | p.Gly442Ser | missense_variant | 8/10 | NP_001189787.1 | ||
ECM1 | NM_022664.3 | c.868G>A | p.Gly290Ser | missense_variant | 7/9 | NP_073155.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ECM1 | ENST00000369047.9 | c.1243G>A | p.Gly415Ser | missense_variant | 8/10 | 1 | NM_004425.4 | ENSP00000358043.4 | ||
ECM1 | ENST00000346569.6 | c.868G>A | p.Gly290Ser | missense_variant | 7/9 | 1 | ENSP00000271630.6 | |||
ECM1 | ENST00000369049.8 | c.1324G>A | p.Gly442Ser | missense_variant | 8/10 | 2 | ENSP00000358045.4 | |||
ECM1 | ENST00000470432.5 | n.2600G>A | non_coding_transcript_exon_variant | 4/6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.334 AC: 50422AN: 151166Hom.: 9088 Cov.: 28
GnomAD3 exomes AF: 0.352 AC: 88524AN: 251444Hom.: 16631 AF XY: 0.359 AC XY: 48816AN XY: 135890
GnomAD4 exome AF: 0.387 AC: 565697AN: 1461846Hom.: 112382 Cov.: 75 AF XY: 0.388 AC XY: 282325AN XY: 727226
GnomAD4 genome AF: 0.333 AC: 50448AN: 151284Hom.: 9096 Cov.: 28 AF XY: 0.332 AC XY: 24510AN XY: 73846
ClinVar
Submissions by phenotype
Lipid proteinosis Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at