rs696116
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001002912.5(ERICH3):c.820-2641T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.054 in 152,188 control chromosomes in the GnomAD database, including 672 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 0.054 ( 672 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
ERICH3
NM_001002912.5 intron
NM_001002912.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.22
Genes affected
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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERICH3 | NM_001002912.5 | c.820-2641T>G | intron_variant | ENST00000326665.10 | |||
ERICH3-AS1 | NR_121671.1 | n.2331A>C | non_coding_transcript_exon_variant | 3/3 | |||
ERICH3 | XM_017000275.2 | c.814-2641T>G | intron_variant | ||||
ERICH3-AS1 | NR_121670.1 | n.2424A>C | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERICH3 | ENST00000326665.10 | c.820-2641T>G | intron_variant | 5 | NM_001002912.5 | P3 | |||
ERICH3 | ENST00000420661.6 | c.229-2641T>G | intron_variant | 1 | A2 | ||||
ERICH3-AS1 | ENST00000612390.4 | n.2331A>C | non_coding_transcript_exon_variant | 3/3 | 1 | ||||
ERICH3 | ENST00000479666.1 | c.229-270T>G | intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0539 AC: 8196AN: 152070Hom.: 672 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
8196
AN:
152070
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 10Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 10
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
10
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
10
Gnomad4 AFR exome
AF:
Gnomad4 NFE exome
AF:
GnomAD4 genome ? AF: 0.0540 AC: 8219AN: 152188Hom.: 672 Cov.: 32 AF XY: 0.0527 AC XY: 3921AN XY: 74430
GnomAD4 genome
?
AF:
AC:
8219
AN:
152188
Hom.:
Cov.:
32
AF XY:
AC XY:
3921
AN XY:
74430
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
51
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at