rs150920473
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_022455.5(NSD1):c.4473G>A(p.Ser1491=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000769 in 1,613,164 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. S1491S) has been classified as Likely benign.
Frequency
Consequence
NM_022455.5 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 |
---|---|---|---|---|---|---|---|
NSD1 | NM_022455.5 | c.4473G>A | p.Ser1491= | synonymous_variant | 10/23 | ENST00000439151.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSD1 | ENST00000439151.7 | c.4473G>A | p.Ser1491= | synonymous_variant | 10/23 | 1 | NM_022455.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000994 AC: 25AN: 251462Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135898
GnomAD4 exome AF: 0.0000753 AC: 110AN: 1460856Hom.: 0 Cov.: 30 AF XY: 0.0000647 AC XY: 47AN XY: 726772
GnomAD4 genome ? AF: 0.0000919 AC: 14AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 01, 2019 | This variant is associated with the following publications: (PMID: 15742365) - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2022 | NSD1: BP4, BP7 - |
Sotos syndrome Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 19, 2022 | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at