rs1322319
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000611278.4(ZNF248):c.-271T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,142,014 control chromosomes in the GnomAD database, including 11,443 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 0.13 ( 1353 hom., cov: 32)
Exomes 𝑓: 0.14 ( 10090 hom. )
Consequence
ZNF248
ENST00000611278.4 5_prime_UTR
ENST00000611278.4 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.332
Genes affected
ZNF248 (HGNC:13041): (zinc finger protein 248) Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.88).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF248 | NM_021045.3 | c.-125-49T>C | intron_variant | ENST00000395867.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF248 | ENST00000395867.8 | c.-125-49T>C | intron_variant | 1 | NM_021045.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.129 AC: 19539AN: 151950Hom.: 1352 Cov.: 32
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GnomAD4 exome AF: 0.141 AC: 139190AN: 989946Hom.: 10090 Cov.: 29 AF XY: 0.141 AC XY: 65422AN XY: 465050
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GnomAD4 genome ? AF: 0.129 AC: 19544AN: 152068Hom.: 1353 Cov.: 32 AF XY: 0.128 AC XY: 9521AN XY: 74318
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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