rs755946624
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_003240.5(LEFTY2):c.348C>T(p.Ala116=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000268 in 1,566,172 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A116A) has been classified as Likely benign.
Frequency
Consequence
NM_003240.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LEFTY2 | NM_003240.5 | c.348C>T | p.Ala116= | synonymous_variant | 2/4 | ENST00000366820.10 | |
LEFTY2 | XM_011544266.2 | c.348C>T | p.Ala116= | synonymous_variant | 2/4 | ||
LEFTY2 | NM_001172425.3 | c.280-34C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LEFTY2 | ENST00000366820.10 | c.348C>T | p.Ala116= | synonymous_variant | 2/4 | 1 | NM_003240.5 | P1 | |
LEFTY2 | ENST00000420304.6 | c.280-34C>T | intron_variant | 2 | |||||
LEFTY2 | ENST00000474493.1 | n.197C>T | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152246Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000572 AC: 9AN: 157386Hom.: 0 AF XY: 0.0000230 AC XY: 2AN XY: 86794
GnomAD4 exome AF: 0.0000177 AC: 25AN: 1413808Hom.: 0 Cov.: 34 AF XY: 0.0000186 AC XY: 13AN XY: 700690
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152364Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74512
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Left-right axis malformations Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at