rs6890783
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001031711.3(ERGIC1):c.21-23396G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0132 in 152,218 control chromosomes in the GnomAD database, including 17 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 0.013 ( 17 hom., cov: 31)
Consequence
ERGIC1
NM_001031711.3 intron
NM_001031711.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.08
Genes affected
ERGIC1 (HGNC:29205): (endoplasmic reticulum-golgi intermediate compartment 1) This gene encodes a cycling membrane protein which is an endoplasmic reticulum-golgi intermediate compartment (ERGIC) protein which interacts with other members of this protein family to increase their turnover. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0132 (2003/152218) while in subpopulation NFE AF= 0.0213 (1447/68004). AF 95% confidence interval is 0.0204. There are 17 homozygotes in gnomad4. There are 911 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 17 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ERGIC1 | NM_001031711.3 | c.21-23396G>A | intron_variant | ENST00000393784.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ERGIC1 | ENST00000393784.8 | c.21-23396G>A | intron_variant | 1 | NM_001031711.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0132 AC: 2006AN: 152100Hom.: 17 Cov.: 31
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0132 AC: 2003AN: 152218Hom.: 17 Cov.: 31 AF XY: 0.0122 AC XY: 911AN XY: 74408
GnomAD4 genome
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911
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74408
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18
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at