rs1714505
Positions:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP4_StrongBS1
The NM_001271838.2(RSRC1):c.653-17830C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000921 in 152,014 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 0.000092 ( 0 hom., cov: 31)
Consequence
RSRC1
NM_001271838.2 intron
NM_001271838.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.349
Genes affected
RSRC1 (HGNC:24152): (arginine and serine rich coiled-coil 1) This gene encodes a member of the serine and arginine rich-related protein family. The encoded protein is involved in both constitutive and alternative mRNA splicing. This gene may be associated with schizophrenia. A pseudogene of this gene is located on chromosome 9. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Nov 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0000921 (14/152014) while in subpopulation NFE AF= 0.000191 (13/67994). AF 95% confidence interval is 0.000112. There are 0 homozygotes in gnomad4. There are 2 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RSRC1 | NM_001271838.2 | c.653-17830C>G | intron_variant | ENST00000611884.5 | |||
RSRC1 | NM_001271834.2 | c.479-17830C>G | intron_variant | ||||
RSRC1 | NM_016625.4 | c.653-17830C>G | intron_variant | ||||
RSRC1 | XM_047448275.1 | c.653-17830C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RSRC1 | ENST00000611884.5 | c.653-17830C>G | intron_variant | 5 | NM_001271838.2 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000921 AC: 14AN: 152014Hom.: 0 Cov.: 31
GnomAD3 genomes
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152014
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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: 0.0000921 AC: 14AN: 152014Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74232
GnomAD4 genome
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152014
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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