rs72639216
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_198880.3(QRICH1):c.*704C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000139 in 324,582 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000035 ( 0 hom. )
Consequence
QRICH1
NM_198880.3 3_prime_UTR
NM_198880.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.46
Genes affected
QRICH1 (HGNC:24713): (glutamine rich 1) Enables DNA binding activity. Involved in several processes, including PERK-mediated unfolded protein response; intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress; and positive regulation of transcription, DNA-templated. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.51).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000256 (39/152196) while in subpopulation AFR AF= 0.000843 (35/41524). AF 95% confidence interval is 0.000622. There are 0 homozygotes in gnomad4. There are 19 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High AC in GnomAd at 39 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
QRICH1 | NM_198880.3 | c.*704C>A | 3_prime_UTR_variant | 10/10 | ENST00000395443.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
QRICH1 | ENST00000395443.7 | c.*704C>A | 3_prime_UTR_variant | 10/10 | 1 | NM_198880.3 | P1 | ||
ENST00000607245.1 | downstream_gene_variant | ||||||||
QRICH1 | ENST00000703871.1 | downstream_gene_variant | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000256 AC: 39AN: 152080Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.0000348 AC: 6AN: 172386Hom.: 0 Cov.: 0 AF XY: 0.0000322 AC XY: 3AN XY: 93136
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GnomAD4 genome ? AF: 0.000256 AC: 39AN: 152196Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74394
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ClinVar
Not reported inComputational scores
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Name
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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