GeneBe

rs11362637

Variant names:

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_018993.4(RIN2):​c.-36-2945_-36-2935delTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000768 in 520,974 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000017 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0000049 ( 0 hom. )

Consequence

RIN2
NM_018993.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.204
Variant links:
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 Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RIN2NM_018993.4 linkc.-36-2945_-36-2935delTTTTTTTTTTT intron_variant Intron 2 of 12 ENST00000255006.12 NP_061866.1 Q8WYP3-1A1A4T0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RIN2ENST00000255006.12 linkc.-36-2945_-36-2935delTTTTTTTTTTT intron_variant Intron 2 of 12 2 NM_018993.4 ENSP00000255006.7 Q8WYP3-1
RIN2ENST00000648440 linkc.-196_-186delTTTTTTTTTTT 5_prime_UTR_variant Exon 1 of 12 ENSP00000498085.1 Q8WYP3-1
RIN2ENST00000432334.2 linkn.537-2945_537-2935delTTTTTTTTTTT intron_variant Intron 3 of 3 4
RIN2ENST00000648165.1 linkn.618-2945_618-2935delTTTTTTTTTTT intron_variant Intron 3 of 3

Frequencies

GnomAD3 genomes
AF:
0.0000173
AC:
2
AN:
115278
Hom.:
0
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.0000681
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000493
AC:
2
AN:
405696
Hom.:
0
AF XY:
0.00000912
AC XY:
2
AN XY:
219210
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000410
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000406
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000173
AC:
2
AN:
115278
Hom.:
0
Cov.:
0
AF XY:
0.0000185
AC XY:
1
AN XY:
54192
show subpopulations
Gnomad4 AFR
AF:
0.0000681
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs11362637; hg19: chr20-19867256; API