NM_000330.4:c.651G>A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_000330.4(RS1):c.651G>A(p.Leu217Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000911 in 1,097,979 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000330.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RS1 | NM_000330.4 | c.651G>A | p.Leu217Leu | synonymous_variant | Exon 6 of 6 | ENST00000379984.4 | NP_000321.1 | |
RS1 | XM_047442337.1 | c.555G>A | p.Leu185Leu | synonymous_variant | Exon 4 of 4 | XP_047298293.1 | ||
CDKL5 | NM_001037343.2 | c.2714-3979C>T | intron_variant | Intron 19 of 21 | NP_001032420.1 | |||
CDKL5 | NM_003159.3 | c.2714-3979C>T | intron_variant | Intron 18 of 20 | NP_003150.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RS1 | ENST00000379984.4 | c.651G>A | p.Leu217Leu | synonymous_variant | Exon 6 of 6 | 1 | NM_000330.4 | ENSP00000369320.3 | ||
CDKL5 | ENST00000379989.6 | c.2714-3979C>T | intron_variant | Intron 19 of 21 | 1 | ENSP00000369325.3 | ||||
CDKL5 | ENST00000379996.7 | c.2714-3979C>T | intron_variant | Intron 18 of 20 | 1 | ENSP00000369332.3 | ||||
RS1 | ENST00000476595.1 | n.1142G>A | non_coding_transcript_exon_variant | Exon 5 of 5 | 1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1097979Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363437
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.