12-19316144-A-G

Variant summary

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

The ENST00000429027.7(PLEKHA5):​c.2118+1250A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.723 in 151,804 control chromosomes in the GnomAD database, including 42,035 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 0.72 ( 42035 hom., cov: 29)

Consequence

PLEKHA5
ENST00000429027.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.403
Variant links:
Genes affected
PLEKHA5 (HGNC:30036): (pleckstrin homology domain containing A5) Predicted to enable phosphatidylinositol phosphate binding activity. Predicted to act upstream of or within reproductive system development. Located in cytosol and nucleoplasm. [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=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.856 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PLEKHA5NM_001256470.2 linkuse as main transcriptc.2118+1250A>G intron_variant ENST00000429027.7 NP_001243399.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PLEKHA5ENST00000429027.7 linkuse as main transcriptc.2118+1250A>G intron_variant 1 NM_001256470.2 ENSP00000404296 A2Q9HAU0-6

Frequencies

GnomAD3 genomes
AF:
0.723
AC:
109727
AN:
151686
Hom.:
42052
Cov.:
29
show subpopulations
Gnomad AFR
AF:
0.479
Gnomad AMI
AF:
0.969
Gnomad AMR
AF:
0.776
Gnomad ASJ
AF:
0.829
Gnomad EAS
AF:
0.399
Gnomad SAS
AF:
0.663
Gnomad FIN
AF:
0.833
Gnomad MID
AF:
0.842
Gnomad NFE
AF:
0.862
Gnomad OTH
AF:
0.758
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.723
AC:
109721
AN:
151804
Hom.:
42035
Cov.:
29
AF XY:
0.719
AC XY:
53316
AN XY:
74198
show subpopulations
Gnomad4 AFR
AF:
0.478
Gnomad4 AMR
AF:
0.775
Gnomad4 ASJ
AF:
0.829
Gnomad4 EAS
AF:
0.398
Gnomad4 SAS
AF:
0.663
Gnomad4 FIN
AF:
0.833
Gnomad4 NFE
AF:
0.862
Gnomad4 OTH
AF:
0.749
Alfa
AF:
0.820
Hom.:
22673
Bravo
AF:
0.710
Asia WGS
AF:
0.482
AC:
1678
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
0.98
DANN
Benign
0.61

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: rs10743315; hg19: chr12-19469078; API