rs882845
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032023.4(RASSF4):c.138+151T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 602,498 control chromosomes in the GnomAD database, including 103,039 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 0.51 ( 21999 hom., cov: 32)
Exomes 𝑓: 0.59 ( 81040 hom. )
Consequence
RASSF4
NM_032023.4 intron
NM_032023.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.43
Genes affected
RASSF4 (HGNC:20793): (Ras association domain family member 4) The function of this gene has not yet been determined but may involve a role in tumor suppression. Alternative splicing of this gene results in several transcript variants; however, most of the variants have not been fully described. [provided by RefSeq, Jul 2008]
DEPP1 (HGNC:23355): (DEPP autophagy regulator 1) The expression of this gene is induced by fasting as well as by progesterone. The protein encoded by this gene contains a t-synaptosome-associated protein receptor (SNARE) coiled-coil homology domain and a peroxisomal targeting signal. Production of the encoded protein leads to phosphorylation and activation of the transcription factor ELK1. [provided by RefSeq, Jul 2008]
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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=-0.79).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RASSF4 | NM_032023.4 | c.138+151T>A | intron_variant | ENST00000340258.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RASSF4 | ENST00000340258.10 | c.138+151T>A | intron_variant | 1 | NM_032023.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.508 AC: 77167AN: 151930Hom.: 21988 Cov.: 32
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GnomAD4 exome AF: 0.589 AC: 265439AN: 450448Hom.: 81040 AF XY: 0.585 AC XY: 138325AN XY: 236566
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GnomAD4 genome ? AF: 0.508 AC: 77203AN: 152050Hom.: 21999 Cov.: 32 AF XY: 0.512 AC XY: 38068AN XY: 74304
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at