rs2287692
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_016154.5(RAB4B):c.275+11G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 1,569,146 control chromosomes in the GnomAD database, including 16,435 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 0.11 ( 1151 hom., cov: 30)
Exomes 𝑓: 0.14 ( 15284 hom. )
Consequence
RAB4B
NM_016154.5 intron
NM_016154.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.601
Genes affected
RAB4B (HGNC:9782): (RAB4B, member RAS oncogene family) Predicted to enable G protein activity and GTP binding activity. Involved in glucose import. Located in insulin-responsive compartment; perinuclear region of cytoplasm; and recycling endosome. [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=-0.83).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAB4B | NM_016154.5 | c.275+11G>A | intron_variant | ENST00000357052.8 | |||
MIA-RAB4B | NR_037775.1 | n.637+11G>A | intron_variant, non_coding_transcript_variant | ||||
RAB4B-EGLN2 | NR_037791.1 | n.432+11G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAB4B | ENST00000357052.8 | c.275+11G>A | intron_variant | 1 | NM_016154.5 | P1 | |||
ENST00000595728.2 | n.992-3960C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.109 AC: 16495AN: 151618Hom.: 1148 Cov.: 30
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GnomAD3 exomes AF: 0.135 AC: 29932AN: 221640Hom.: 2269 AF XY: 0.140 AC XY: 16652AN XY: 119332
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GnomAD4 exome AF: 0.144 AC: 203498AN: 1417412Hom.: 15284 Cov.: 46 AF XY: 0.145 AC XY: 101309AN XY: 699468
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GnomAD4 genome ? AF: 0.109 AC: 16507AN: 151734Hom.: 1151 Cov.: 30 AF XY: 0.110 AC XY: 8133AN XY: 74130
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ClinVar
Not reported inComputational scores
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Name
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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