chrX-110681668-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001143981.2(CHRDL1):c.989-19A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0016 in 1,164,584 control chromosomes in the GnomAD database, including 34 homozygotes. There are 547 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0024 ( 5 hom., 91 hem., cov: 23)
Exomes 𝑓: 0.0015 ( 29 hom. 456 hem. )
Consequence
CHRDL1
NM_001143981.2 intron
NM_001143981.2 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.188
Genes affected
CHRDL1 (HGNC:29861): (chordin like 1) This gene encodes an antagonist of bone morphogenetic protein 4. The encoded protein may play a role in topographic retinotectal projection and in the regulation of retinal angiogenesis in response to hypoxia. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jan 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant X-110681668-T-C is Benign according to our data. Variant chrX-110681668-T-C is described in ClinVar as [Benign]. Clinvar id is 1987026.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00235 (265/112628) while in subpopulation EAS AF= 0.017 (61/3582). AF 95% confidence interval is 0.0149. There are 5 homozygotes in gnomad4. There are 91 alleles in male gnomad4 subpopulation. Median coverage is 23. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 5 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRDL1 | NM_001143981.2 | c.989-19A>G | intron_variant | ENST00000372042.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRDL1 | ENST00000372042.6 | c.989-19A>G | intron_variant | 2 | NM_001143981.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00236 AC: 266AN: 112572Hom.: 5 Cov.: 23 AF XY: 0.00265 AC XY: 92AN XY: 34716
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GnomAD3 exomes AF: 0.00392 AC: 656AN: 167179Hom.: 7 AF XY: 0.00259 AC XY: 143AN XY: 55119
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GnomAD4 exome AF: 0.00152 AC: 1598AN: 1051956Hom.: 29 Cov.: 24 AF XY: 0.00141 AC XY: 456AN XY: 323600
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 17, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
La Branchor
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at