rs2994809
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032044.4(REG4):c.-94-491A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 152,176 control chromosomes in the GnomAD database, including 62,943 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 0.91 ( 62943 hom., cov: 33)
Consequence
REG4
NM_032044.4 intron
NM_032044.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.960
Genes affected
REG4 (HGNC:22977): (regenerating family member 4) Enables heparin binding activity and mannan binding activity. Predicted to act upstream of or within response to bacterium. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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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 = 0.959 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
REG4 | NM_032044.4 | c.-94-491A>G | intron_variant | ENST00000256585.10 | |||
REG4 | NM_001159352.2 | c.-268-152A>G | intron_variant | ||||
REG4 | NM_001159353.2 | c.-94-491A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
REG4 | ENST00000256585.10 | c.-94-491A>G | intron_variant | 1 | NM_032044.4 | P1 | |||
REG4 | ENST00000354219.5 | c.-268-152A>G | intron_variant | 1 | P1 | ||||
REG4 | ENST00000369401.4 | c.-94-491A>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.906 AC: 137691AN: 152058Hom.: 62891 Cov.: 33
GnomAD3 genomes
?
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137691
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.906 AC: 137798AN: 152176Hom.: 62943 Cov.: 33 AF XY: 0.903 AC XY: 67163AN XY: 74406
GnomAD4 genome
?
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137798
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152176
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33
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67163
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74406
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2529
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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