chr10-68284159-G-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022129.4(PBLD):c.*18C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 1,589,032 control chromosomes in the GnomAD database, including 41,628 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 0.25 ( 5329 hom., cov: 32)
Exomes 𝑓: 0.22 ( 36299 hom. )
Consequence
PBLD
NM_022129.4 3_prime_UTR
NM_022129.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.17
Genes affected
PBLD (HGNC:23301): (phenazine biosynthesis like protein domain containing) Enables identical protein binding activity. Involved in maintenance of gastrointestinal epithelium; negative regulation of SMAD protein signal transduction; and negative regulation of transforming growth factor beta receptor signaling pathway. Located in cytoplasm. [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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PBLD | NM_022129.4 | c.*18C>T | 3_prime_UTR_variant | 10/10 | ENST00000358769.7 | ||
PBLD | XM_005270028.5 | c.*18C>T | 3_prime_UTR_variant | 10/10 | |||
PBLD | XM_011540060.4 | c.*38C>T | 3_prime_UTR_variant | 10/10 | |||
PBLD | XM_017016513.2 | c.*38C>T | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PBLD | ENST00000358769.7 | c.*18C>T | 3_prime_UTR_variant | 10/10 | 5 | NM_022129.4 | P1 | ||
PBLD | ENST00000309049.8 | c.*18C>T | 3_prime_UTR_variant | 10/10 | 1 | P1 | |||
PBLD | ENST00000336578.5 | c.*18C>T | 3_prime_UTR_variant | 8/8 | 1 | ||||
PBLD | ENST00000468798.5 | c.213-869C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.253 AC: 38429AN: 151880Hom.: 5320 Cov.: 32
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GnomAD3 exomes AF: 0.274 AC: 66975AN: 244402Hom.: 10534 AF XY: 0.267 AC XY: 35307AN XY: 132298
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GnomAD4 exome AF: 0.216 AC: 309861AN: 1437034Hom.: 36299 Cov.: 27 AF XY: 0.217 AC XY: 155637AN XY: 716070
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GnomAD4 genome AF: 0.253 AC: 38461AN: 151998Hom.: 5329 Cov.: 32 AF XY: 0.261 AC XY: 19417AN XY: 74278
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ClinVar
Not reported inComputational scores
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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