rs12555631
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002171.2(IFNA10):c.*100C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 1,563,850 control chromosomes in the GnomAD database, including 27,112 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 ( 3237 hom., cov: 32)
Exomes 𝑓: 0.17 ( 23875 hom. )
Consequence
IFNA10
NM_002171.2 3_prime_UTR
NM_002171.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.21
Genes affected
IFNA10 (HGNC:5418): (interferon alpha 10) This gene encodes a protein that belongs to the type I interferon family of proteins, and is located in a cluster of alpha interferon genes on chromosome 9. Interferons are small regulatory molecules that function in cell signaling in response to viruses and other pathogens or tumor cells. This gene is intronless and the encoded protein is secreted. [provided by RefSeq, Aug 2013]
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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=-0.93).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IFNA10 | NM_002171.2 | c.*100C>T | 3_prime_UTR_variant | 1/1 | ENST00000357374.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IFNA10 | ENST00000357374.2 | c.*100C>T | 3_prime_UTR_variant | 1/1 | NM_002171.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.196 AC: 29806AN: 151746Hom.: 3236 Cov.: 32
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GnomAD4 exome AF: 0.174 AC: 246302AN: 1411986Hom.: 23875 Cov.: 28 AF XY: 0.172 AC XY: 120688AN XY: 701482
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GnomAD4 genome ? AF: 0.196 AC: 29831AN: 151864Hom.: 3237 Cov.: 32 AF XY: 0.197 AC XY: 14657AN XY: 74246
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ClinVar
Not reported inComputational scores
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Name
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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