rs7614311
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001355236.2(C3orf49):c.570+253A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 152,002 control chromosomes in the GnomAD database, including 1,910 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 0.15 ( 1910 hom., cov: 32)
Consequence
C3orf49
NM_001355236.2 intron
NM_001355236.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.620
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C3orf49 | NM_001355236.2 | c.570+253A>C | intron_variant | ENST00000295896.13 | |||
C3orf49 | XM_024453353.2 | c.570+253A>C | intron_variant | ||||
C3orf49 | XM_047447470.1 | c.366+253A>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C3orf49 | ENST00000295896.13 | c.570+253A>C | intron_variant | 2 | NM_001355236.2 | A2 | |||
C3orf49 | ENST00000491896.1 | c.195+253A>C | intron_variant | 2 | |||||
C3orf49 | ENST00000647022.1 | c.570+253A>C | intron_variant | P2 | |||||
C3orf49 | ENST00000673037.1 | c.437+253A>C | intron_variant |
Frequencies
GnomAD3 genomes ? AF: 0.152 AC: 23029AN: 151884Hom.: 1909 Cov.: 32
GnomAD3 genomes
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23029
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.152 AC: 23038AN: 152002Hom.: 1910 Cov.: 32 AF XY: 0.150 AC XY: 11136AN XY: 74316
GnomAD4 genome
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23038
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152002
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32
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11136
AN XY:
74316
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398
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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
DS_AG_spliceai
Position offset: 16
Find out detailed SpliceAI scores and Pangolin per-transcript scores at