1-225937471-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_003240.5(LEFTY2):c.1071G>A(p.Gly357=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000284 in 1,613,932 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. G357G) 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 -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LEFTY2 | NM_003240.5 | c.1071G>A | p.Gly357= | synonymous_variant | 4/4 | ENST00000366820.10 | |
LEFTY2 | NM_001172425.3 | c.969G>A | p.Gly323= | synonymous_variant | 5/5 | ||
LEFTY2 | XM_011544266.2 | c.*444G>A | 3_prime_UTR_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LEFTY2 | ENST00000366820.10 | c.1071G>A | p.Gly357= | synonymous_variant | 4/4 | 1 | NM_003240.5 | P1 | |
ENST00000513672.1 | n.87G>A | non_coding_transcript_exon_variant | 1/2 | 2 | |||||
LEFTY2 | ENST00000420304.6 | c.969G>A | p.Gly323= | synonymous_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000328 AC: 50AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000526 AC: 132AN: 251122Hom.: 0 AF XY: 0.000515 AC XY: 70AN XY: 135850
GnomAD4 exome AF: 0.000280 AC: 409AN: 1461720Hom.: 1 Cov.: 29 AF XY: 0.000261 AC XY: 190AN XY: 727162
GnomAD4 genome ? AF: 0.000328 AC: 50AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.000444 AC XY: 33AN XY: 74366
ClinVar
Submissions by phenotype
Left-right axis malformations Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at