rs587783962
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_133433.4(NIPBL):c.5211G>A(p.Gln1737Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,386 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 Benign (★).
Frequency
Consequence
NM_133433.4 synonymous
Scores
Clinical Significance
Conservation
Publications
- Cornelia de Lange syndromeInheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen
- Cornelia de Lange syndrome 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
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ACMG classification
Our verdict: Benign. The variant received -9 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_133433.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NIPBL | NM_133433.4 | MANE Select | c.5211G>A | p.Gln1737Gln | synonymous | Exon 26 of 47 | NP_597677.2 | ||
| NIPBL | NM_001438586.1 | c.5211G>A | p.Gln1737Gln | synonymous | Exon 26 of 47 | NP_001425515.1 | |||
| NIPBL | NM_015384.5 | c.5211G>A | p.Gln1737Gln | synonymous | Exon 26 of 46 | NP_056199.2 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| NIPBL | ENST00000282516.13 | TSL:1 MANE Select | c.5211G>A | p.Gln1737Gln | synonymous | Exon 26 of 47 | ENSP00000282516.8 | ||
| NIPBL | ENST00000448238.2 | TSL:1 | c.5211G>A | p.Gln1737Gln | synonymous | Exon 26 of 46 | ENSP00000406266.2 | ||
| NIPBL | ENST00000652901.1 | c.5211G>A | p.Gln1737Gln | synonymous | Exon 26 of 46 | ENSP00000499536.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD2 exomes AF: 0.00000796 AC: 2AN: 251240 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461386Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727028 show subpopulations
Age Distribution
GnomAD4 genome Cov.: 33
ClinVar
ClinVar submissions as Germline
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at