chr19-36007185-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001039876.3(SYNE4):c.363G>A(p.Gln121Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00158 in 1,585,708 control chromosomes in the GnomAD database, including 33 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.363G>A | p.Gln121Gln | synonymous_variant | Exon 3 of 8 | ENST00000324444.9 | NP_001034965.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00839 AC: 1278AN: 152264Hom.: 16 Cov.: 32
GnomAD3 exomes AF: 0.00195 AC: 387AN: 198468Hom.: 6 AF XY: 0.00148 AC XY: 159AN XY: 107572
GnomAD4 exome AF: 0.000853 AC: 1222AN: 1433326Hom.: 17 Cov.: 35 AF XY: 0.000764 AC XY: 543AN XY: 710536
GnomAD4 genome AF: 0.00839 AC: 1278AN: 152382Hom.: 16 Cov.: 32 AF XY: 0.00858 AC XY: 639AN XY: 74518
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
Gln121Gln in exon 3 of SYNE4: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue and is not located with in the splice consensus sequence. It has been identified in 2.4% (97/3984) of Af rican American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs73607773). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at