rs11121182

Positions:

Variant summary

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

The ENST00000400908.7(RERE):​c.1203+3432G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,224 control chromosomes in the GnomAD database, including 2,411 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 0.17 ( 2411 hom., cov: 32)

Consequence

RERE
ENST00000400908.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.819
Variant links:
Genes affected
RERE (HGNC:9965): (arginine-glutamic acid dipeptide repeats) This gene encodes a member of the atrophin family of arginine-glutamic acid (RE) dipeptide repeat-containing proteins. The encoded protein co-localizes with a transcription factor in the nucleus, and its overexpression triggers apoptosis. A similar protein in mouse associates with histone deacetylase and is thought to function as a transcriptional co-repressor during embryonic development. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

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=-0.89).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RERENM_001042681.2 linkuse as main transcriptc.1203+3432G>T intron_variant ENST00000400908.7 NP_001036146.1
RERENM_012102.4 linkuse as main transcriptc.1203+3432G>T intron_variant NP_036234.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
REREENST00000400908.7 linkuse as main transcriptc.1203+3432G>T intron_variant 1 NM_001042681.2 ENSP00000383700 P1Q9P2R6-1

Frequencies

GnomAD3 genomes
AF:
0.167
AC:
25394
AN:
152106
Hom.:
2409
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0832
Gnomad AMI
AF:
0.308
Gnomad AMR
AF:
0.233
Gnomad ASJ
AF:
0.228
Gnomad EAS
AF:
0.109
Gnomad SAS
AF:
0.170
Gnomad FIN
AF:
0.171
Gnomad MID
AF:
0.268
Gnomad NFE
AF:
0.200
Gnomad OTH
AF:
0.220
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.167
AC:
25401
AN:
152224
Hom.:
2411
Cov.:
32
AF XY:
0.166
AC XY:
12350
AN XY:
74452
show subpopulations
Gnomad4 AFR
AF:
0.0831
Gnomad4 AMR
AF:
0.233
Gnomad4 ASJ
AF:
0.228
Gnomad4 EAS
AF:
0.109
Gnomad4 SAS
AF:
0.171
Gnomad4 FIN
AF:
0.171
Gnomad4 NFE
AF:
0.200
Gnomad4 OTH
AF:
0.220
Alfa
AF:
0.206
Hom.:
3412
Bravo
AF:
0.170
Asia WGS
AF:
0.159
AC:
553
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.93
DANN
Benign
0.53

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs11121182; hg19: chr1-8522553; COSMIC: COSV61939177; COSMIC: COSV61939177; API