NM_182914.3:c.13707+10T>C
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_182914.3(SYNE2):c.13707+10T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0171 in 1,614,110 control chromosomes in the GnomAD database, including 276 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_182914.3 intron
Scores
Clinical Significance
Conservation
Publications
- male infertility with azoospermia or oligozoospermia due to single gene mutationInheritance: AR Classification: MODERATE Submitted by: King Faisal Specialist Hospital and Research Center
- familial medullary thyroid carcinomaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- ovarian dysgenesis 8Inheritance: AD, Unknown Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNE2 | NM_182914.3 | c.13707+10T>C | intron_variant | Intron 72 of 115 | ENST00000555002.6 | NP_878918.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNE2 | ENST00000555002.6 | c.13707+10T>C | intron_variant | Intron 72 of 115 | 1 | NM_182914.3 | ENSP00000450831.2 |
Frequencies
GnomAD3 genomes AF: 0.0225 AC: 3427AN: 152172Hom.: 46 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0168 AC: 4213AN: 251078 AF XY: 0.0171 show subpopulations
GnomAD4 exome AF: 0.0166 AC: 24222AN: 1461820Hom.: 230 Cov.: 32 AF XY: 0.0167 AC XY: 12115AN XY: 727196 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0225 AC: 3433AN: 152290Hom.: 46 Cov.: 32 AF XY: 0.0228 AC XY: 1699AN XY: 74458 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Emery-Dreifuss muscular dystrophy 5, autosomal dominant Benign:3
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This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not specified Benign:2
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not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at