chr14-92649065-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024832.5(RIN3):​c.533-2517G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,168 control chromosomes in the GnomAD database, including 54,081 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 0.84 ( 54081 hom., cov: 31)

Consequence

RIN3
NM_024832.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.31
Variant links:
Genes affected
RIN3 (HGNC:18751): (Ras and Rab interactor 3) Summary: This protein encoded by this gene is a member of the RIN family of Ras interaction-interference proteins, which are binding partners to the RAB5 small GTPases. The protein functions as a guanine nucleotide exchange for RAB5B and RAB31. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RIN3NM_024832.5 linkc.533-2517G>C intron_variant ENST00000216487.12 NP_079108.3 Q8TB24-1Q6NSK7Q86U22
RIN3NM_001319987.2 linkc.308-2517G>C intron_variant NP_001306916.1 Q8TB24Q6ZRC2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RIN3ENST00000216487.12 linkc.533-2517G>C intron_variant 1 NM_024832.5 ENSP00000216487.7 Q8TB24-1
RIN3ENST00000555589.5 linkn.460-2517G>C intron_variant 1 ENSP00000450682.1 G3V2I7
RIN3ENST00000620541.4 linkc.533-2517G>C intron_variant 5 ENSP00000480603.1 A0A087WWY9
RIN3ENST00000418924.6 linkn.432-2517G>C intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.842
AC:
127983
AN:
152050
Hom.:
54027
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.855
Gnomad AMI
AF:
0.749
Gnomad AMR
AF:
0.880
Gnomad ASJ
AF:
0.801
Gnomad EAS
AF:
0.997
Gnomad SAS
AF:
0.850
Gnomad FIN
AF:
0.849
Gnomad MID
AF:
0.807
Gnomad NFE
AF:
0.815
Gnomad OTH
AF:
0.841
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.842
AC:
128097
AN:
152168
Hom.:
54081
Cov.:
31
AF XY:
0.845
AC XY:
62897
AN XY:
74392
show subpopulations
Gnomad4 AFR
AF:
0.855
Gnomad4 AMR
AF:
0.880
Gnomad4 ASJ
AF:
0.801
Gnomad4 EAS
AF:
0.997
Gnomad4 SAS
AF:
0.850
Gnomad4 FIN
AF:
0.849
Gnomad4 NFE
AF:
0.815
Gnomad4 OTH
AF:
0.843
Alfa
AF:
0.796
Hom.:
2475
Bravo
AF:
0.846
Asia WGS
AF:
0.889
AC:
3089
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
0.085
DANN
Benign
0.46

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs754388; hg19: chr14-93115410; API