chrX-154404839-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001303620.2(DNASE1L1):c.300G>A(p.Val100=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,209,959 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000018 ( 0 hom., 2 hem., cov: 24)
Exomes 𝑓: 0.000015 ( 0 hom. 5 hem. )
Consequence
DNASE1L1
NM_001303620.2 synonymous
NM_001303620.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0110
Genes affected
DNASE1L1 (HGNC:2957): (deoxyribonuclease 1 like 1) This gene encodes a deoxyribonuclease protein that shows high sequence similarity to DNase I. The encoded protein is localized to the endoplasmic reticulum and modified by N-linked glycosylation. Alternate transcriptional splice variants encoding the same protein have been observed. [provided by RefSeq, Jan 2015]
RPL10 (HGNC:10298): (ribosomal protein L10) This gene encodes a ribosomal protein that is a component of the 60S ribosome subunit. The related protein in chicken can bind to c-Jun and can repress c-Jun-mediated transcriptional activation. Some studies have detected an association between variation in this gene and autism spectrum disorders, though others do not detect this relationship. There are multiple pseudogenes of this gene dispersed throughout the genome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant X-154404839-C-T is Benign according to our data. Variant chrX-154404839-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2661804.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Hemizygotes in GnomAd at 2 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNASE1L1 | NM_001303620.2 | c.300G>A | p.Val100= | synonymous_variant | 4/8 | ENST00000369807.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNASE1L1 | ENST00000369807.6 | c.300G>A | p.Val100= | synonymous_variant | 4/8 | 1 | NM_001303620.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000178 AC: 2AN: 112547Hom.: 0 Cov.: 24 AF XY: 0.0000576 AC XY: 2AN XY: 34707
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GnomAD3 exomes AF: 0.00000552 AC: 1AN: 181192Hom.: 0 AF XY: 0.0000151 AC XY: 1AN XY: 66422
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GnomAD4 exome AF: 0.0000146 AC: 16AN: 1097412Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 5AN XY: 362988
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | DNASE1L1: BS2 - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
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Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 7
Find out detailed SpliceAI scores and Pangolin per-transcript scores at