rs367909431
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000344408.10(EVC2):c.1470+25G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000162 in 1,612,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00012 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00017 ( 0 hom. )
Consequence
EVC2
ENST00000344408.10 intron
ENST00000344408.10 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.53
Genes affected
EVC2 (HGNC:19747): (EvC ciliary complex subunit 2) This gene encodes a protein that functions in bone formation and skeletal development. Mutations in this gene, as well as in a neighboring gene that lies in a head-to-head configuration, cause Ellis-van Creveld syndrome, an autosomal recessive skeletal dysplasia that is also known as chondroectodermal dysplasia. Mutations in this gene also cause acrofacial dysostosis Weyers type, also referred to as Curry-Hall syndrome, a disease that combines limb and facial abnormalities. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.0).
BP6
Variant 4-5640489-C-T is Benign according to our data. Variant chr4-5640489-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 262604.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EVC2 | NM_147127.5 | c.1470+25G>A | intron_variant | ENST00000344408.10 | NP_667338.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EVC2 | ENST00000344408.10 | c.1470+25G>A | intron_variant | 1 | NM_147127.5 | ENSP00000342144 | P2 | |||
EVC2 | ENST00000310917.6 | c.1230+25G>A | intron_variant | 1 | ENSP00000311683 | A2 | ||||
EVC2 | ENST00000475313.5 | c.1230+25G>A | intron_variant, NMD_transcript_variant | 1 | ENSP00000431981 | |||||
EVC2 | ENST00000509670.1 | c.1222+33G>A | intron_variant, NMD_transcript_variant | 1 | ENSP00000423876 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 151990Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000112 AC: 28AN: 250624Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135452
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GnomAD4 exome AF: 0.000167 AC: 244AN: 1460844Hom.: 0 Cov.: 32 AF XY: 0.000157 AC XY: 114AN XY: 726852
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GnomAD4 genome AF: 0.000118 AC: 18AN: 152108Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74354
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Benign
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Benign
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