rs12479213
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_198963.3(DHX57):c.-7+1720G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,784 control chromosomes in the GnomAD database, including 4,156 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 0.20 ( 4156 hom., cov: 31)
Consequence
DHX57
NM_198963.3 intron
NM_198963.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.212
Genes affected
DHX57 (HGNC:20086): (DExH-box helicase 57) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DHX57 | NM_198963.3 | c.-7+1720G>T | intron_variant | ENST00000457308.6 | NP_945314.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DHX57 | ENST00000457308.6 | c.-7+1720G>T | intron_variant | 1 | NM_198963.3 | ENSP00000405111.2 | ||||
DHX57 | ENST00000474104.5 | n.93+1720G>T | intron_variant | 1 | ||||||
DHX57 | ENST00000622155.4 | n.139+1720G>T | intron_variant | 1 | ||||||
DHX57 | ENST00000619207.1 | c.-83+1720G>T | intron_variant | 4 | ENSP00000479840.1 |
Frequencies
GnomAD3 genomes AF: 0.200 AC: 30399AN: 151668Hom.: 4159 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: 0.200 AC: 30397AN: 151784Hom.: 4156 Cov.: 31 AF XY: 0.207 AC XY: 15373AN XY: 74178
GnomAD4 genome
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31
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74178
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Asia WGS
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1182
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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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at