rs2285424
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001039876.3(SYNE4):c.225G>A(p.Pro75Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 1,605,578 control chromosomes in the GnomAD database, including 39,697 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001039876.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNE4 | NM_001039876.3 | c.225G>A | p.Pro75Pro | synonymous_variant | Exon 2 of 8 | ENST00000324444.9 | NP_001034965.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.295 AC: 44863AN: 151876Hom.: 8819 Cov.: 31
GnomAD3 exomes AF: 0.228 AC: 54961AN: 240750Hom.: 8013 AF XY: 0.212 AC XY: 27633AN XY: 130522
GnomAD4 exome AF: 0.191 AC: 278208AN: 1453586Hom.: 30840 Cov.: 32 AF XY: 0.189 AC XY: 136304AN XY: 722614
GnomAD4 genome AF: 0.296 AC: 44957AN: 151992Hom.: 8857 Cov.: 31 AF XY: 0.298 AC XY: 22130AN XY: 74278
ClinVar
Submissions by phenotype
not specified Benign:2
Pro75Pro in exon 2 of SYNE4: This variant is not expected to have clinical signi ficance because it does not alter an amino acid residue and is not located withi n the splice consensus sequence. It has been identified in 47.5% (1845/3886) of African American chromosomes from a broad population by the NHLBI Exome Sequenci ng Project (http://evs.gs.washington.edu/EVS; dbSNP rs2285424). -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:2
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Autosomal recessive nonsyndromic hearing loss 76 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at