rs10497323
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_152381.6(XIRP2):āc.1836T>Cā(p.Gly612Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 1,613,762 control chromosomes in the GnomAD database, including 36,887 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: š 0.28 ( 7638 hom., cov: 32)
Exomes š: 0.19 ( 29249 hom. )
Consequence
XIRP2
NM_152381.6 synonymous
NM_152381.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.321
Genes affected
XIRP2 (HGNC:14303): (xin actin binding repeat containing 2) Enables actin filament binding activity. Predicted to be involved in actin cytoskeleton organization and heart development. Predicted to act upstream of or within cardiac muscle tissue morphogenesis; cell-cell junction organization; and ventricular septum development. Colocalizes with focal adhesion and stress fiber. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.58).
BP6
Variant 2-167243228-T-C is Benign according to our data. Variant chr2-167243228-T-C is described in ClinVar as [Benign]. Clinvar id is 3058991.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr2-167243228-T-C is described in Lovd as [Benign].
BP7
Synonymous conserved (PhyloP=0.321 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
XIRP2 | NM_152381.6 | c.1836T>C | p.Gly612Gly | synonymous_variant | 9/11 | ENST00000409195.6 | NP_689594.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
XIRP2 | ENST00000409195.6 | c.1836T>C | p.Gly612Gly | synonymous_variant | 9/11 | 5 | NM_152381.6 | ENSP00000386840.2 |
Frequencies
GnomAD3 genomes AF: 0.278 AC: 42180AN: 151860Hom.: 7605 Cov.: 32
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GnomAD3 exomes AF: 0.225 AC: 56032AN: 249314Hom.: 7448 AF XY: 0.222 AC XY: 29981AN XY: 135244
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GnomAD4 exome AF: 0.185 AC: 271133AN: 1461784Hom.: 29249 Cov.: 36 AF XY: 0.187 AC XY: 135920AN XY: 727194
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GnomAD4 genome AF: 0.278 AC: 42273AN: 151978Hom.: 7638 Cov.: 32 AF XY: 0.279 AC XY: 20756AN XY: 74268
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
XIRP2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 21, 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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at