rs2285422
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001039876.3(SYNE4):āc.834G>Cā(p.Gln278His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.94 in 1,612,406 control chromosomes in the GnomAD database, including 713,595 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Consequence
NM_001039876.3 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 | UniProt |
---|---|---|---|---|---|---|---|
SYNE4 | NM_001039876.3 | c.834G>C | p.Gln278His | missense_variant | 5/8 | ENST00000324444.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYNE4 | ENST00000324444.9 | c.834G>C | p.Gln278His | missense_variant | 5/8 | 5 | NM_001039876.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.950 AC: 144518AN: 152078Hom.: 68818 Cov.: 31
GnomAD3 exomes AF: 0.927 AC: 228734AN: 246814Hom.: 106346 AF XY: 0.924 AC XY: 123911AN XY: 134106
GnomAD4 exome AF: 0.939 AC: 1371128AN: 1460210Hom.: 644717 Cov.: 82 AF XY: 0.937 AC XY: 680221AN XY: 726308
GnomAD4 genome ? AF: 0.950 AC: 144638AN: 152196Hom.: 68878 Cov.: 31 AF XY: 0.948 AC XY: 70536AN XY: 74406
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 24, 2014 | Gln278His in exon 5 of SYNE4: This variant is not expected to have clinical sign ificance because it has been identified in 4.9% (402/8232) of European American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs2285422). - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 09, 2017 | 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. - |
Autosomal recessive nonsyndromic hearing loss 76 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at