rs6046396
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018993.4(RIN2):c.-36-17707G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,048 control chromosomes in the GnomAD database, including 35,544 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 0.68 ( 35543 hom., cov: 32)
Exomes 𝑓: 1.0 ( 1 hom. )
Consequence
RIN2
NM_018993.4 intron
NM_018993.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0260
Genes affected
RIN2 (HGNC:18750): (Ras and Rab interactor 2) The RAB5 protein is a small GTPase involved in membrane trafficking in the early endocytic pathway. The protein encoded by this gene binds the GTP-bound form of the RAB5 protein preferentially over the GDP-bound form, and functions as a guanine nucleotide exchange factor for RAB5. The encoded protein is found primarily as a tetramer in the cytoplasm and does not bind other members of the RAB family. Mutations in this gene cause macrocephaly alopecia cutis laxa and scoliosis (MACS) syndrome, an elastic tissue disorder, as well as the related connective tissue disorder, RIN2 syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2011]
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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 = 0.701 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RIN2 | NM_018993.4 | c.-36-17707G>A | intron_variant | ENST00000255006.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIN2 | ENST00000255006.12 | c.-36-17707G>A | intron_variant | 2 | NM_018993.4 | P1 | |||
RIN2 | ENST00000616029.2 | n.1208G>A | non_coding_transcript_exon_variant | 4/4 | |||||
RIN2 | ENST00000432334.2 | n.537-17707G>A | intron_variant, non_coding_transcript_variant | 4 | |||||
RIN2 | ENST00000648165.1 | n.617+564G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.683 AC: 103735AN: 151926Hom.: 35520 Cov.: 32
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GnomAD4 exome AF: 1.00 AC: 2AN: 2Hom.: 1 Cov.: 0AC XY: 0AN XY: 0
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GnomAD4 genome ? AF: 0.683 AC: 103813AN: 152046Hom.: 35543 Cov.: 32 AF XY: 0.679 AC XY: 50484AN XY: 74342
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ClinVar
Not reported inComputational scores
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Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at