rs7125115
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001144758.3(PHLDB1):c.-106G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 144,560 control chromosomes in the GnomAD database, including 13,259 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 0.41 ( 13254 hom., cov: 23)
Exomes 𝑓: 0.16 ( 5 hom. )
Consequence
PHLDB1
NM_001144758.3 5_prime_UTR
NM_001144758.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0570
Genes affected
PHLDB1 (HGNC:23697): (pleckstrin homology like domain family B member 1) Involved in regulation of embryonic development; regulation of epithelial to mesenchymal transition; and regulation of microtubule cytoskeleton organization. Located in basal cortex. [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=-0.67).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHLDB1 | NM_001144758.3 | c.-106G>A | 5_prime_UTR_variant | 1/23 | ENST00000600882.6 | ||
LOC124902765 | XR_007062908.1 | n.390-427C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHLDB1 | ENST00000600882.6 | c.-106G>A | 5_prime_UTR_variant | 1/23 | 1 | NM_001144758.3 |
Frequencies
GnomAD3 genomes ? AF: 0.411 AC: 59312AN: 144238Hom.: 13234 Cov.: 23
GnomAD3 genomes
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GnomAD4 exome AF: 0.160 AC: 34AN: 212Hom.: 5 Cov.: 0 AF XY: 0.141 AC XY: 20AN XY: 142
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GnomAD4 genome ? AF: 0.411 AC: 59363AN: 144348Hom.: 13254 Cov.: 23 AF XY: 0.408 AC XY: 28543AN XY: 70006
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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