rs890835
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014901.5(RNF44):c.1236+18T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 1,608,772 control chromosomes in the GnomAD database, including 623,582 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 0.90 ( 62523 hom., cov: 34)
Exomes 𝑓: 0.88 ( 561059 hom. )
Consequence
RNF44
NM_014901.5 intron
NM_014901.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -7.23
Genes affected
RNF44 (HGNC:19180): (ring finger protein 44) The protein encoded by this gene contains a RING finger, a motif present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions. [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=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNF44 | NM_014901.5 | c.1236+18T>G | intron_variant | ENST00000274811.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNF44 | ENST00000274811.9 | c.1236+18T>G | intron_variant | 1 | NM_014901.5 | P1 | |||
RNF44 | ENST00000506378.1 | c.519T>G | p.Ser173= | synonymous_variant | 5/5 | 2 | |||
RNF44 | ENST00000515051.1 | n.404T>G | non_coding_transcript_exon_variant | 2/2 | 4 | ||||
RNF44 | ENST00000513029.5 | c.*1034+18T>G | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.904 AC: 137602AN: 152200Hom.: 62460 Cov.: 34
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GnomAD3 exomes AF: 0.860 AC: 214793AN: 249740Hom.: 93031 AF XY: 0.853 AC XY: 115408AN XY: 135308
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GnomAD4 exome AF: 0.876 AC: 1276126AN: 1456454Hom.: 561059 Cov.: 32 AF XY: 0.871 AC XY: 631490AN XY: 724848
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GnomAD4 genome ? AF: 0.904 AC: 137727AN: 152318Hom.: 62523 Cov.: 34 AF XY: 0.901 AC XY: 67078AN XY: 74472
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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