rs141550472
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_182914.3(SYNE2):āc.19581A>Cā(p.Lys6527Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000201 in 1,614,122 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Consequence
NM_182914.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SYNE2 | NM_182914.3 | c.19581A>C | p.Lys6527Asn | missense_variant | 109/116 | ENST00000555002.6 | NP_878918.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SYNE2 | ENST00000555002.6 | c.19581A>C | p.Lys6527Asn | missense_variant | 109/116 | 1 | NM_182914.3 | ENSP00000450831.2 |
Frequencies
GnomAD3 genomes AF: 0.00106 AC: 162AN: 152194Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000362 AC: 91AN: 251350Hom.: 0 AF XY: 0.000236 AC XY: 32AN XY: 135842
GnomAD4 exome AF: 0.000112 AC: 163AN: 1461810Hom.: 0 Cov.: 31 AF XY: 0.0000853 AC XY: 62AN XY: 727198
GnomAD4 genome AF: 0.00106 AC: 162AN: 152312Hom.: 1 Cov.: 32 AF XY: 0.000873 AC XY: 65AN XY: 74474
ClinVar
Submissions by phenotype
Emery-Dreifuss muscular dystrophy 5, autosomal dominant Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at