chr16-57207890-A-AC
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_133368.3(RSPRY1):c.351-167dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.035 in 152,242 control chromosomes in the GnomAD database, including 101 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.035 ( 101 hom., cov: 31)
Consequence
RSPRY1
NM_133368.3 intron
NM_133368.3 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.753
Genes affected
RSPRY1 (HGNC:29420): (ring finger and SPRY domain containing 1) This gene encodes a glycoprotein that contains a RING-type zinc finger domain and an SPRY domain of unknown function. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 16-57207890-A-AC is Benign according to our data. Variant chr16-57207890-A-AC is described in ClinVar as [Benign]. Clinvar id is 1259854.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.035 (5328/152242) while in subpopulation NFE AF= 0.0378 (2568/68002). AF 95% confidence interval is 0.0365. There are 101 homozygotes in gnomad4. There are 2694 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 100 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RSPRY1 | NM_133368.3 | c.351-167dup | intron_variant | ENST00000394420.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RSPRY1 | ENST00000394420.9 | c.351-167dup | intron_variant | 1 | NM_133368.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0350 AC: 5330AN: 152124Hom.: 100 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0350 AC: 5328AN: 152242Hom.: 101 Cov.: 31 AF XY: 0.0362 AC XY: 2694AN XY: 74460
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?
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74460
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 16, 2021 | - - |
Computational scores
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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