rs2282611
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000658868.1(EMSY-DT):n.396+476A>C 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 0.27 in 152,072 control chromosomes in the GnomAD database, including 5,849 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 0.27 ( 5849 hom., cov: 32)
Consequence
EMSY-DT
ENST00000658868.1 intron, non_coding_transcript
ENST00000658868.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.553
Genes affected
EMSY-DT (HGNC:55507): (EMSY divergent transcript)
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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=-0.81).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC124902718 | XR_007062786.1 | n.403+476A>C | intron_variant, non_coding_transcript_variant | ||||
LOC124902718 | XR_007062787.1 | n.476+403A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EMSY-DT | ENST00000658868.1 | n.396+476A>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.270 AC: 41063AN: 151954Hom.: 5845 Cov.: 32
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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: 0.270 AC: 41071AN: 152072Hom.: 5849 Cov.: 32 AF XY: 0.269 AC XY: 19985AN XY: 74326
GnomAD4 genome
?
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41071
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32
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19985
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74326
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663
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at