chr16-84850594-C-T
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_031476.4(CRISPLD2):c.519C>T(p.Ile173=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000813 in 1,614,148 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0041 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00047 ( 6 hom. )
Consequence
CRISPLD2
NM_031476.4 synonymous
NM_031476.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.48
Genes affected
CRISPLD2 (HGNC:25248): (cysteine rich secretory protein LCCL domain containing 2) Predicted to enable glycosaminoglycan binding activity. Involved in face morphogenesis. Located in transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 16-84850594-C-T is Benign according to our data. Variant chr16-84850594-C-T is described in ClinVar as [Benign]. Clinvar id is 777049.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-2.48 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 6 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRISPLD2 | NM_031476.4 | c.519C>T | p.Ile173= | synonymous_variant | 5/15 | ENST00000262424.10 | |
CRISPLD2 | XM_005256190.2 | c.519C>T | p.Ile173= | synonymous_variant | 6/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRISPLD2 | ENST00000262424.10 | c.519C>T | p.Ile173= | synonymous_variant | 5/15 | 1 | NM_031476.4 | P4 | |
ENST00000648152.1 | n.373-1760G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00410 AC: 624AN: 152168Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00107 AC: 269AN: 251474Hom.: 2 AF XY: 0.000758 AC XY: 103AN XY: 135904
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GnomAD4 exome AF: 0.000469 AC: 686AN: 1461862Hom.: 6 Cov.: 31 AF XY: 0.000406 AC XY: 295AN XY: 727236
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GnomAD4 genome AF: 0.00412 AC: 627AN: 152286Hom.: 1 Cov.: 32 AF XY: 0.00387 AC XY: 288AN XY: 74450
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jul 06, 2018 | - - |
CRISPLD2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 07, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
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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