rs17334002

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014935.5(PLEKHA6):​c.-95+22713A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,232 control chromosomes in the GnomAD database, including 3,382 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 0.19 ( 3382 hom., cov: 32)

Consequence

PLEKHA6
NM_014935.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19

Publications

3 publications found
Variant links:
Genes affected
PLEKHA6 (HGNC:17053): (pleckstrin homology domain containing A6)
PLEKHA6 Gene-Disease associations (from GenCC):
  • schizophrenia
    Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PLEKHA6NM_014935.5 linkc.-95+22713A>G intron_variant Intron 1 of 22 ENST00000272203.8 NP_055750.2 Q9Y2H5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PLEKHA6ENST00000272203.8 linkc.-95+22713A>G intron_variant Intron 1 of 22 1 NM_014935.5 ENSP00000272203.2 Q9Y2H5

Frequencies

GnomAD3 genomes
AF:
0.193
AC:
29409
AN:
152114
Hom.:
3381
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0791
Gnomad AMI
AF:
0.208
Gnomad AMR
AF:
0.170
Gnomad ASJ
AF:
0.151
Gnomad EAS
AF:
0.129
Gnomad SAS
AF:
0.238
Gnomad FIN
AF:
0.291
Gnomad MID
AF:
0.114
Gnomad NFE
AF:
0.257
Gnomad OTH
AF:
0.196
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.193
AC:
29415
AN:
152232
Hom.:
3382
Cov.:
32
AF XY:
0.195
AC XY:
14511
AN XY:
74426
show subpopulations
African (AFR)
AF:
0.0789
AC:
3280
AN:
41558
American (AMR)
AF:
0.170
AC:
2596
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.151
AC:
524
AN:
3468
East Asian (EAS)
AF:
0.130
AC:
674
AN:
5186
South Asian (SAS)
AF:
0.238
AC:
1146
AN:
4824
European-Finnish (FIN)
AF:
0.291
AC:
3083
AN:
10584
Middle Eastern (MID)
AF:
0.122
AC:
36
AN:
294
European-Non Finnish (NFE)
AF:
0.257
AC:
17475
AN:
68000
Other (OTH)
AF:
0.194
AC:
411
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1218
2436
3655
4873
6091
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
318
636
954
1272
1590
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.231
Hom.:
13082
Bravo
AF:
0.176
Asia WGS
AF:
0.184
AC:
639
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
CADD
Benign
0.20
DANN
Benign
0.76
PhyloP100
-1.2
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs17334002; hg19: chr1-204306109; API