chr5-35644519-T-C
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_024867.4(SPEF2):āc.579T>Cā(p.Ile193=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 1,591,038 control chromosomes in the GnomAD database, including 356,525 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
Frequency
Genomes: š 0.70 ( 37557 hom., cov: 32)
Exomes š: 0.66 ( 318968 hom. )
Consequence
SPEF2
NM_024867.4 synonymous
NM_024867.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.13
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BP6
Variant 5-35644519-T-C is Benign according to our data. Variant chr5-35644519-T-C is described in ClinVar as [Benign]. Clinvar id is 403472.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.13 with no splicing effect.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPEF2 | NM_024867.4 | c.579T>C | p.Ile193= | synonymous_variant | 4/37 | ENST00000356031.8 | NP_079143.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPEF2 | ENST00000356031.8 | c.579T>C | p.Ile193= | synonymous_variant | 4/37 | 1 | NM_024867.4 | ENSP00000348314 | P2 |
Frequencies
GnomAD3 genomes AF: 0.698 AC: 106056AN: 151918Hom.: 37496 Cov.: 32
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GnomAD3 exomes AF: 0.707 AC: 162203AN: 229368Hom.: 58134 AF XY: 0.703 AC XY: 87402AN XY: 124254
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GnomAD4 exome AF: 0.663 AC: 953405AN: 1439002Hom.: 318968 Cov.: 33 AF XY: 0.666 AC XY: 476156AN XY: 715286
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GnomAD4 genome AF: 0.698 AC: 106183AN: 152036Hom.: 37557 Cov.: 32 AF XY: 0.699 AC XY: 51961AN XY: 74298
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 04, 2021 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 29, 2016 | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency - |
Spermatogenic failure 43 Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
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BayesDel_noAF
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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