rs389967

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001329630.2(PLEKHA7):​c.523-708C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,198 control chromosomes in the GnomAD database, including 891 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 0.10 ( 891 hom., cov: 33)

Consequence

PLEKHA7
NM_001329630.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.16
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PLEKHA7NM_001329630.2 linkuse as main transcriptc.523-708C>T intron_variant ENST00000531066.6 NP_001316559.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PLEKHA7ENST00000531066.6 linkuse as main transcriptc.523-708C>T intron_variant 5 NM_001329630.2 ENSP00000435389 A1

Frequencies

GnomAD3 genomes
AF:
0.103
AC:
15628
AN:
152080
Hom.:
892
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0657
Gnomad AMI
AF:
0.0735
Gnomad AMR
AF:
0.143
Gnomad ASJ
AF:
0.143
Gnomad EAS
AF:
0.159
Gnomad SAS
AF:
0.118
Gnomad FIN
AF:
0.0643
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.115
Gnomad OTH
AF:
0.118
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.103
AC:
15631
AN:
152198
Hom.:
891
Cov.:
33
AF XY:
0.101
AC XY:
7533
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.0656
Gnomad4 AMR
AF:
0.144
Gnomad4 ASJ
AF:
0.143
Gnomad4 EAS
AF:
0.159
Gnomad4 SAS
AF:
0.118
Gnomad4 FIN
AF:
0.0643
Gnomad4 NFE
AF:
0.115
Gnomad4 OTH
AF:
0.117
Alfa
AF:
0.116
Hom.:
251
Bravo
AF:
0.110
Asia WGS
AF:
0.129
AC:
449
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
8.6
DANN
Benign
0.63

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs389967; hg19: chr11-16874610; API