rs2992
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005483.3(CHAF1A):c.*24T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 1,425,146 control chromosomes in the GnomAD database, including 71,557 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 0.33 ( 8630 hom., cov: 33)
Exomes 𝑓: 0.31 ( 62927 hom. )
Consequence
CHAF1A
NM_005483.3 3_prime_UTR
NM_005483.3 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.41
Genes affected
CHAF1A (HGNC:1910): (chromatin assembly factor 1 subunit A) Chromatin assembly factor I (CAF1) is a nuclear complex consisting of p50, p60 (CHAF1B; MIM 601245), and p150 (CHAF1A) subunits that assembles histone octamers onto replicating DNA in vitro (Kaufman et al., 1995 [PubMed 7600578]).[supplied by OMIM, Mar 2008]
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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 (EAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHAF1A | NM_005483.3 | c.*24T>C | 3_prime_UTR_variant | 15/15 | ENST00000301280.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHAF1A | ENST00000301280.10 | c.*24T>C | 3_prime_UTR_variant | 15/15 | 1 | NM_005483.3 | P1 | ||
CHAF1A | ENST00000589648.1 | c.88+708T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.327 AC: 49715AN: 151966Hom.: 8616 Cov.: 33
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GnomAD3 exomes AF: 0.364 AC: 62847AN: 172860Hom.: 12384 AF XY: 0.356 AC XY: 32463AN XY: 91116
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GnomAD4 exome AF: 0.306 AC: 389397AN: 1273062Hom.: 62927 Cov.: 19 AF XY: 0.306 AC XY: 194533AN XY: 635432
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GnomAD4 genome ? AF: 0.327 AC: 49757AN: 152084Hom.: 8630 Cov.: 33 AF XY: 0.333 AC XY: 24757AN XY: 74346
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at