chr16-67147456-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_025187.5(PHAF1):c.*325G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00506 in 313,300 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0048 ( 9 hom., cov: 32)
Exomes 𝑓: 0.0053 ( 5 hom. )
Consequence
PHAF1
NM_025187.5 3_prime_UTR
NM_025187.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.20
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
?
Variant 16-67147456-G-A is Benign according to our data. Variant chr16-67147456-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2646609.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 9 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHAF1 | NM_025187.5 | c.*325G>A | 3_prime_UTR_variant | 16/16 | ENST00000219139.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHAF1 | ENST00000219139.8 | c.*325G>A | 3_prime_UTR_variant | 16/16 | 1 | NM_025187.5 | P1 | ||
PHAF1 | ENST00000569277.1 | c.270G>A | p.Gly90= | synonymous_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00480 AC: 730AN: 152206Hom.: 9 Cov.: 32
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GnomAD3 exomes AF: 0.00329 AC: 64AN: 19450Hom.: 1 AF XY: 0.00392 AC XY: 38AN XY: 9690
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GnomAD4 exome AF: 0.00532 AC: 856AN: 160976Hom.: 5 Cov.: 0 AF XY: 0.00509 AC XY: 415AN XY: 81486
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GnomAD4 genome ? AF: 0.00479 AC: 730AN: 152324Hom.: 9 Cov.: 32 AF XY: 0.00509 AC XY: 379AN XY: 74484
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | PHAF1: BS2 - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at