2-36356616-T-C
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Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_016441.3(CRIM1):āc.324T>Cā(p.Val108=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000657 in 1,606,594 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 (ā ).
Frequency
Genomes: š 0.0026 ( 3 hom., cov: 32)
Exomes š: 0.00046 ( 4 hom. )
Consequence
CRIM1
NM_016441.3 synonymous
NM_016441.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.418
Genes affected
CRIM1 (HGNC:2359): (cysteine rich transmembrane BMP regulator 1) This gene encodes a transmembrane protein containing six cysteine-rich repeat domains and an insulin-like growth factor-binding domain. The encoded protein may play a role in tissue development though interactions with members of the transforming growth factor beta family, such as bone morphogenetic proteins. [provided by RefSeq, Nov 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.72).
BP6
Variant 2-36356616-T-C is Benign according to our data. Variant chr2-36356616-T-C is described in ClinVar as [Benign]. Clinvar id is 708457.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.418 with no splicing effect.
BS2
High Homozygotes in GnomAd4 at 3 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRIM1 | NM_016441.3 | c.324T>C | p.Val108= | synonymous_variant | 1/17 | ENST00000280527.7 | NP_057525.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRIM1 | ENST00000280527.7 | c.324T>C | p.Val108= | synonymous_variant | 1/17 | 1 | NM_016441.3 | ENSP00000280527 | P1 | |
CRIM1 | ENST00000426856.1 | c.174T>C | p.Val58= | synonymous_variant | 1/4 | 3 | ENSP00000407636 | |||
CRIM1 | ENST00000428774.1 | c.147T>C | p.Val49= | synonymous_variant | 1/2 | 3 | ENSP00000415706 |
Frequencies
GnomAD3 genomes AF: 0.00257 AC: 389AN: 151616Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00131 AC: 315AN: 240974Hom.: 4 AF XY: 0.00123 AC XY: 162AN XY: 132124
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GnomAD4 exome AF: 0.000458 AC: 667AN: 1454860Hom.: 4 Cov.: 31 AF XY: 0.000506 AC XY: 366AN XY: 723552
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GnomAD4 genome AF: 0.00256 AC: 388AN: 151734Hom.: 3 Cov.: 32 AF XY: 0.00226 AC XY: 168AN XY: 74194
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
CRIM1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 28, 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
CADD
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DANN
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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