rs202220730
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_022455.5(NSD1):āc.7421A>Cā(p.Gln2474Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000049 in 1,613,500 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_022455.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSD1 | NM_022455.5 | c.7421A>C | p.Gln2474Pro | missense_variant | 23/23 | ENST00000439151.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSD1 | ENST00000439151.7 | c.7421A>C | p.Gln2474Pro | missense_variant | 23/23 | 1 | NM_022455.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152234Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000180 AC: 45AN: 250464Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135428
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1461148Hom.: 0 Cov.: 34 AF XY: 0.0000385 AC XY: 28AN XY: 726932
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152352Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74516
ClinVar
Submissions by phenotype
Sotos syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Sep 22, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Nov 29, 2021 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at