rs61571386
Positions:
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-A
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
- chr3-47101597-AGTGTGTGTGTGTGTGTGTGTGTGT-AGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The NM_014159.7(SETD2):c.4918-66_4918-43del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000504 in 734,106 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. There are indicators that this mutation may affect the branch point..
Frequency
Genomes: 𝑓 0.0000071 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000061 ( 1 hom. )
Consequence
SETD2
NM_014159.7 intron
NM_014159.7 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.26
Genes affected
SETD2 (HGNC:18420): (SET domain containing 2, histone lysine methyltransferase) Huntington's disease (HD), a neurodegenerative disorder characterized by loss of striatal neurons, is caused by an expansion of a polyglutamine tract in the HD protein huntingtin. This gene encodes a protein belonging to a class of huntingtin interacting proteins characterized by WW motifs. This protein is a histone methyltransferase that is specific for lysine-36 of histone H3, and methylation of this residue is associated with active chromatin. This protein also contains a novel transcriptional activation domain and has been found associated with hyperphosphorylated RNA polymerase II. [provided by RefSeq, Aug 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population sas. gnomad4_exome allele frequency = 0.0000608 (36/592436) while in subpopulation SAS AF= 0.000664 (34/51190). AF 95% confidence interval is 0.000488. There are 1 homozygotes in gnomad4_exome. There are 32 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
BS2
High AC in GnomAdExome4 at 36 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SETD2 | NM_014159.7 | c.4918-66_4918-43del | intron_variant | ENST00000409792.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SETD2 | ENST00000409792.4 | c.4918-66_4918-43del | intron_variant | 5 | NM_014159.7 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00000706 AC: 1AN: 141572Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.0000608 AC: 36AN: 592436Hom.: 1 AF XY: 0.000101 AC XY: 32AN XY: 315700
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GnomAD4 genome AF: 0.00000706 AC: 1AN: 141670Hom.: 0 Cov.: 0 AF XY: 0.0000146 AC XY: 1AN XY: 68672
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ClinVar
Not reported inComputational scores
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Score
Prediction
BranchPoint Hunter
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at