rs3214051
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000356769.7(NACA):c.-192C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.617 in 152,198 control chromosomes in the GnomAD database, including 29,433 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 0.62 ( 29406 hom., cov: 33)
Exomes 𝑓: 0.74 ( 27 hom. )
Consequence
NACA
ENST00000356769.7 5_prime_UTR
ENST00000356769.7 5_prime_UTR
Scores
2
Splicing: ADA: 0.00003699
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.139
Genes affected
NACA (HGNC:7629): (nascent polypeptide associated complex subunit alpha) This gene encodes a protein that associates with basic transcription factor 3 (BTF3) to form the nascent polypeptide-associated complex (NAC). This complex binds to nascent proteins that lack a signal peptide motif as they emerge from the ribosome, blocking interaction with the signal recognition particle (SRP) and preventing mistranslocation to the endoplasmic reticulum. This protein is an IgE autoantigen in atopic dermatitis patients. Alternative splicing results in multiple transcript variants, but the full length nature of some of these variants, including those encoding very large proteins, has not been determined. There are multiple pseudogenes of this gene on different chromosomes. [provided by RefSeq, Feb 2016]
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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=-0.79).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NACA | ENST00000356769.7 | c.-192C>T | 5_prime_UTR_variant | 1/8 | 1 | P4 | |||
NACA | ENST00000546392.6 | c.-218C>T | 5_prime_UTR_variant | 1/8 | 2 | P4 | |||
NACA | ENST00000549855.5 | c.-192C>T | splice_region_variant, 5_prime_UTR_variant | 2/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.617 AC: 93808AN: 151990Hom.: 29400 Cov.: 33
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GnomAD4 exome AF: 0.744 AC: 67AN: 90Hom.: 27 Cov.: 0 AF XY: 0.703 AC XY: 45AN XY: 64
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GnomAD4 genome ? AF: 0.617 AC: 93849AN: 152108Hom.: 29406 Cov.: 33 AF XY: 0.624 AC XY: 46402AN XY: 74380
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at