rs712507
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001134438.2(PHLDB2):c.2131-2933T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.688 in 152,112 control chromosomes in the GnomAD database, including 36,412 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 0.69 ( 36412 hom., cov: 33)
Consequence
PHLDB2
NM_001134438.2 intron
NM_001134438.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.412
Genes affected
PHLDB2 (HGNC:29573): (pleckstrin homology like domain family B member 2) Enables cadherin binding activity. Involved in several processes, including negative regulation of focal adhesion assembly; regulation of cytoskeleton organization; and regulation of embryonic development. Located in several cellular components, including basal cortex; cell leading edge; and intermediate filament cytoskeleton. Colocalizes with focal adhesion. [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=-0.84).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHLDB2 | NM_001134438.2 | c.2131-2933T>C | intron_variant | ENST00000431670.7 | |||
PHLDB2 | NM_001134437.2 | c.2083-2933T>C | intron_variant | ||||
PHLDB2 | NM_001134439.2 | c.2131-2933T>C | intron_variant | ||||
PHLDB2 | NM_145753.2 | c.2002-2933T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHLDB2 | ENST00000431670.7 | c.2131-2933T>C | intron_variant | 1 | NM_001134438.2 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.688 AC: 104631AN: 151994Hom.: 36372 Cov.: 33
GnomAD3 genomes
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151994
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.688 AC: 104719AN: 152112Hom.: 36412 Cov.: 33 AF XY: 0.689 AC XY: 51234AN XY: 74400
GnomAD4 genome
?
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104719
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33
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51234
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74400
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2834
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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