rs7206971
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152347.5(EFCAB13):c.518-59G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 1,242,976 control chromosomes in the GnomAD database, including 141,622 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.47 ( 16827 hom., cov: 32)
Exomes 𝑓: 0.47 ( 124795 hom. )
Consequence
EFCAB13
NM_152347.5 intron
NM_152347.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.21
Genes affected
EFCAB13 (HGNC:26864): (EF-hand calcium binding domain 13)
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EFCAB13 | NM_152347.5 | c.518-59G>A | intron_variant | ENST00000331493.7 | NP_689560.3 | |||
EFCAB13 | NM_001195192.2 | c.517+2651G>A | intron_variant | NP_001182121.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
EFCAB13 | ENST00000331493.7 | c.518-59G>A | intron_variant | 1 | NM_152347.5 | ENSP00000332111.2 | ||||
EFCAB13 | ENST00000517484.5 | c.517+2651G>A | intron_variant | 2 | ENSP00000430048.1 | |||||
EFCAB13 | ENST00000517310.5 | c.73+2651G>A | intron_variant | 2 | ENSP00000466136.1 | |||||
EFCAB13 | ENST00000520776.5 | n.651+2651G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.466 AC: 70806AN: 151942Hom.: 16822 Cov.: 32
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GnomAD4 exome AF: 0.475 AC: 517744AN: 1090916Hom.: 124795 AF XY: 0.475 AC XY: 250760AN XY: 527942
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GnomAD4 genome AF: 0.466 AC: 70845AN: 152060Hom.: 16827 Cov.: 32 AF XY: 0.462 AC XY: 34322AN XY: 74344
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
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