chr11-16783795-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001329630.2(PLEKHA7):c.3555C>T(p.Tyr1185=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00185 in 1,512,736 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0029 ( 13 hom., cov: 33)
Exomes 𝑓: 0.0017 ( 51 hom. )
Consequence
PLEKHA7
NM_001329630.2 synonymous
NM_001329630.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.25
Genes affected
PLEKHA7 (HGNC:27049): (pleckstrin homology domain containing A7) Enables delta-catenin binding activity. Involved in epithelial cell-cell adhesion; pore complex assembly; and zonula adherens maintenance. Located in several cellular components, including centrosome; nucleoplasm; and zonula adherens. Part of pore complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
?
Variant 11-16783795-G-A is Benign according to our data. Variant chr11-16783795-G-A is described in ClinVar as [Benign]. Clinvar id is 3044870.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=-1.25 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00286 (435/152340) while in subpopulation EAS AF= 0.0388 (201/5174). AF 95% confidence interval is 0.0345. There are 13 homozygotes in gnomad4. There are 225 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 13 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLEKHA7 | NM_001329630.2 | c.3555C>T | p.Tyr1185= | synonymous_variant | 25/27 | ENST00000531066.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLEKHA7 | ENST00000531066.6 | c.3555C>T | p.Tyr1185= | synonymous_variant | 25/27 | 5 | NM_001329630.2 | A1 | |
PLEKHA7 | ENST00000698836.1 | c.3558C>T | p.Tyr1186= | synonymous_variant | 25/27 | P3 | |||
PLEKHA7 | ENST00000637162.1 | c.3189C>T | p.Tyr1063= | synonymous_variant | 21/23 | 5 | |||
PLEKHA7 | ENST00000636090.1 | c.1221C>T | p.Tyr407= | synonymous_variant | 9/12 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00289 AC: 440AN: 152222Hom.: 13 Cov.: 33
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GnomAD3 exomes AF: 0.00735 AC: 841AN: 114362Hom.: 17 AF XY: 0.00590 AC XY: 370AN XY: 62678
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GnomAD4 exome AF: 0.00174 AC: 2370AN: 1360396Hom.: 51 Cov.: 31 AF XY: 0.00164 AC XY: 1098AN XY: 670662
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
PLEKHA7-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 23, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at