rs1488935
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_023034.2(NSD3):c.4072+21C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.22 in 1,610,792 control chromosomes in the GnomAD database, including 40,206 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.21 ( 3707 hom., cov: 32)
Exomes 𝑓: 0.22 ( 36499 hom. )
Consequence
NSD3
NM_023034.2 intron
NM_023034.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.89
Genes affected
NSD3 (HGNC:12767): (nuclear receptor binding SET domain protein 3) This gene is related to the Wolf-Hirschhorn syndrome candidate-1 gene and encodes a protein with PWWP (proline-tryptophan-tryptophan-proline) domains. This protein methylates histone H3 at lysine residues 4 and 27, which represses gene transcription. Two alternatively spliced variants have been described. [provided by RefSeq, May 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.71).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NSD3 | NM_023034.2 | c.4072+21C>T | intron_variant | ENST00000317025.13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NSD3 | ENST00000317025.13 | c.4072+21C>T | intron_variant | 1 | NM_023034.2 | P4 | |||
ENST00000529325.1 | n.37-186G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.214 AC: 32583AN: 152034Hom.: 3692 Cov.: 32
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GnomAD3 exomes AF: 0.207 AC: 51195AN: 246750Hom.: 5503 AF XY: 0.201 AC XY: 26907AN XY: 133780
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GnomAD4 exome AF: 0.221 AC: 321771AN: 1458640Hom.: 36499 Cov.: 31 AF XY: 0.217 AC XY: 157241AN XY: 725436
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GnomAD4 genome AF: 0.215 AC: 32642AN: 152152Hom.: 3707 Cov.: 32 AF XY: 0.210 AC XY: 15594AN XY: 74388
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at