19-36008586-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001039876.3(SYNE4):c.96C>T(p.Thr32Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,613,952 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely 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.96C>T | p.Thr32Thr | synonymous_variant | Exon 1 of 8 | ENST00000324444.9 | NP_001034965.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00145 AC: 220AN: 152150Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00230 AC: 573AN: 249074Hom.: 3 AF XY: 0.00213 AC XY: 288AN XY: 135150
GnomAD4 exome AF: 0.000971 AC: 1420AN: 1461684Hom.: 11 Cov.: 31 AF XY: 0.000963 AC XY: 700AN XY: 727128
GnomAD4 genome AF: 0.00144 AC: 219AN: 152268Hom.: 3 Cov.: 32 AF XY: 0.00203 AC XY: 151AN XY: 74458
ClinVar
Submissions by phenotype
not provided Benign:2
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not specified Benign:1
p.Thr32Thr in exon 1 of SYNE4: This variant is not expected to have clinical sig nificance because it has been identified in 1.3 % (86/6534) of Finnish chromosom es by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; db SNP rs138787817). -
SYNE4-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at