chr11-65868041-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS1
The NM_016938.5(EFEMP2):c.990G>A(p.Pro330Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000168 in 1,613,722 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_016938.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EFEMP2 | NM_016938.5 | c.990G>A | p.Pro330Pro | synonymous_variant | Exon 10 of 11 | ENST00000307998.11 | NP_058634.4 | |
EFEMP2 | NR_037718.2 | n.1115G>A | non_coding_transcript_exon_variant | Exon 10 of 12 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000921 AC: 140AN: 152090Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000291 AC: 73AN: 250474Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135550
GnomAD4 exome AF: 0.0000889 AC: 130AN: 1461514Hom.: 1 Cov.: 31 AF XY: 0.0000674 AC XY: 49AN XY: 727044
GnomAD4 genome AF: 0.000926 AC: 141AN: 152208Hom.: 1 Cov.: 33 AF XY: 0.000914 AC XY: 68AN XY: 74398
ClinVar
Submissions by phenotype
not provided Uncertain:2
BS1, PP3 -
Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function -
Cutis laxa, autosomal recessive, type 1B Benign:1
- -
Cardiovascular phenotype Benign:1
This alteration is classified as 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