rs17629216
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018939.4(PCDHB6):c.*186G>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 0.0478 in 458,712 control chromosomes in the GnomAD database, including 599 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 0.044 ( 179 hom., cov: 32)
Exomes 𝑓: 0.049 ( 420 hom. )
Consequence
PCDHB6
NM_018939.4 3_prime_UTR
NM_018939.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.199
Genes affected
PCDHB6 (HGNC:8691): (protocadherin beta 6) This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. Unlike the alpha and gamma clusters, the transcripts from these genes do not share common 3' exons. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell neural connections. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
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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=-0.81).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0567 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDHB6 | NM_018939.4 | c.*186G>A | 3_prime_UTR_variant | 1/1 | ENST00000231136.4 | ||
PCDHB6 | NM_001303145.2 | c.*186G>A | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDHB6 | ENST00000231136.4 | c.*186G>A | 3_prime_UTR_variant | 1/1 | NM_018939.4 | P1 | |||
ENST00000624192.1 | n.73-15645C>T | intron_variant, non_coding_transcript_variant | 5 | ||||||
ENST00000624802.1 | n.364+19605C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0445 AC: 6733AN: 151466Hom.: 179 Cov.: 32
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GnomAD4 exome AF: 0.0495 AC: 15193AN: 307130Hom.: 420 Cov.: 5 AF XY: 0.0501 AC XY: 7750AN XY: 154614
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GnomAD4 genome ? AF: 0.0444 AC: 6734AN: 151582Hom.: 179 Cov.: 32 AF XY: 0.0432 AC XY: 3200AN XY: 74012
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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