rs11996715

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000623655.2(ERICD):​n.912C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,132 control chromosomes in the GnomAD database, including 14,739 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 0.42 ( 14738 hom., cov: 33)
Exomes 𝑓: 0.43 ( 1 hom. )

Consequence

ERICD
ENST00000623655.2 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

14 publications found
Variant links:
Genes affected
ERICD (HGNC:49404): (E2F1-regulated inhibitor of cell death)
AGO2 (HGNC:3263): (argonaute RISC catalytic component 2) This gene encodes a member of the Argonaute family of proteins which play a role in RNA interference. The encoded protein is highly basic, and contains a PAZ domain and a PIWI domain. It may interact with dicer1 and play a role in short-interfering-RNA-mediated gene silencing. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
AGO2 Gene-Disease associations (from GenCC):
  • Lessel-Kreienkamp syndrome
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Illumina, Labcorp Genetics (formerly Invitae), ClinGen

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ERICDNR_170171.1 linkn.2958C>A non_coding_transcript_exon_variant Exon 1 of 1
AGO2XM_011516968.3 linkc.-117+5001G>T intron_variant Intron 1 of 18 XP_011515270.3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ERICDENST00000623655.2 linkn.912C>A non_coding_transcript_exon_variant Exon 1 of 1 6

Frequencies

GnomAD3 genomes
AF:
0.424
AC:
64384
AN:
152000
Hom.:
14732
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.244
Gnomad AMI
AF:
0.592
Gnomad AMR
AF:
0.408
Gnomad ASJ
AF:
0.567
Gnomad EAS
AF:
0.390
Gnomad SAS
AF:
0.445
Gnomad FIN
AF:
0.466
Gnomad MID
AF:
0.532
Gnomad NFE
AF:
0.519
Gnomad OTH
AF:
0.483
GnomAD4 exome
AF:
0.429
AC:
6
AN:
14
Hom.:
1
Cov.:
0
AF XY:
0.417
AC XY:
5
AN XY:
12
show subpopulations
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AF:
0.500
AC:
1
AN:
2
European-Finnish (FIN)
AF:
0.375
AC:
3
AN:
8
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.500
AC:
2
AN:
4
Other (OTH)
AC:
0
AN:
0
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
1
1
2
2
3
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.423
AC:
64408
AN:
152118
Hom.:
14738
Cov.:
33
AF XY:
0.424
AC XY:
31506
AN XY:
74366
show subpopulations
African (AFR)
AF:
0.244
AC:
10129
AN:
41512
American (AMR)
AF:
0.407
AC:
6220
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.567
AC:
1967
AN:
3470
East Asian (EAS)
AF:
0.390
AC:
2017
AN:
5166
South Asian (SAS)
AF:
0.447
AC:
2156
AN:
4820
European-Finnish (FIN)
AF:
0.466
AC:
4928
AN:
10568
Middle Eastern (MID)
AF:
0.531
AC:
156
AN:
294
European-Non Finnish (NFE)
AF:
0.519
AC:
35272
AN:
67982
Other (OTH)
AF:
0.486
AC:
1024
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1851
3702
5553
7404
9255
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
598
1196
1794
2392
2990
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.467
Hom.:
10566
Bravo
AF:
0.415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.77
DANN
Benign
0.32
PhyloP100
-1.5

Splicing

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

Publications

Other links and lift over

dbSNP: rs11996715; hg19: chr8-141647291; API