rs11868378
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_110847.1(SOCS3-DT):n.327-880G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,064 control chromosomes in the GnomAD database, including 41,626 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 0.74 ( 41626 hom., cov: 31)
Consequence
SOCS3-DT
NR_110847.1 intron, non_coding_transcript
NR_110847.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.615
Genes affected
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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=-1.03).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SOCS3-DT | NR_110847.1 | n.327-880G>A | intron_variant, non_coding_transcript_variant | ||||
SOCS3-DT | NR_110845.1 | n.354G>A | non_coding_transcript_exon_variant | 2/4 | |||
SOCS3-DT | NR_110846.1 | n.59+733G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SOCS3-DT | ENST00000592569.1 | n.322-880G>A | intron_variant, non_coding_transcript_variant | 3 | |||||
SOCS3-DT | ENST00000687996.2 | n.399-880G>A | intron_variant, non_coding_transcript_variant | ||||||
SOCS3-DT | ENST00000689065.1 | n.355-880G>A | intron_variant, non_coding_transcript_variant | ||||||
SOCS3-DT | ENST00000691100.1 | n.600+733G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.736 AC: 111803AN: 151946Hom.: 41600 Cov.: 31
GnomAD3 genomes
?
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111803
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151946
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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: 0.736 AC: 111875AN: 152064Hom.: 41626 Cov.: 31 AF XY: 0.733 AC XY: 54469AN XY: 74310
GnomAD4 genome
?
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111875
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152064
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31
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54469
AN XY:
74310
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2124
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at