11-65870552-G-A
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_016938.5(EFEMP2):c.474C>T(p.Ile158=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,613,826 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. I158I) has been classified as Likely benign.
Frequency
Consequence
NM_016938.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFEMP2 | NM_016938.5 | c.474C>T | p.Ile158= | synonymous_variant | 5/11 | ENST00000307998.11 | |
EFEMP2 | NR_037718.2 | n.599C>T | non_coding_transcript_exon_variant | 5/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFEMP2 | ENST00000307998.11 | c.474C>T | p.Ile158= | synonymous_variant | 5/11 | 1 | NM_016938.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152036Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250818Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135654
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461790Hom.: 0 Cov.: 34 AF XY: 0.0000138 AC XY: 10AN XY: 727190
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152036Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74242
ClinVar
Submissions by phenotype
Cutis laxa, autosomal recessive, type 1B Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 10, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Jul 31, 2018 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 23, 2020 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 02, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at