dbSNP rs16853272: PLEKHA6:c.-94-36899A>G (chr1-204311708-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_014935.5(PLEKHA6):c.-94-36899A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.022 in 931,728 control chromosomes in the GnomAD database, including 257 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 0.022 ( 42 hom., cov: 32)

Exomes 𝑓: 0.022 ( 215 hom. )

Consequence

PLEKHA6
NM_014935.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.575

Publications

0 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)

PLEKHA6 links:

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=-0.61).

BS1

Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0224 (3412/152356) while in subpopulation SAS AF = 0.0304 (147/4830). AF 95% confidence interval is 0.0264. There are 42 homozygotes in GnomAd4. There are 1603 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 42 Unknown gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLEKHA6	NM_014935.5 link	c.-94-36899A>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
PLEKHA6	ENST00000272203.8 link	c.-94-36899A>G		intron_variant	Intron 1 of 22	1	NM_014935.5	ENSP00000272203.2		Q9Y2H5

Frequencies

GnomAD3 genomes

AF:

0.0224

AC:

3410

AN:

152238

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0234

Gnomad AMI

AF:

0.0230

Gnomad AMR

AF:

0.0223

Gnomad ASJ

AF:

0.0372

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0304

Gnomad FIN

AF:

0.00828

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0240

Gnomad OTH

AF:

0.0296

GnomAD4 exome

AF:

0.0219

AC:

17054

AN:

779372

Hom.:

215

Cov.:

AF XY:

0.0217

AC XY:

7841

AN XY:

361190

show subpopulations

African (AFR)

AF:

0.0231

AC:

342

AN:

14828

American (AMR)

AF:

0.0142

AC:

AN:

918

Ashkenazi Jewish (ASJ)

AF:

0.0393

AC:

189

AN:

4814

East Asian (EAS)

AF:

0.000293

AC:

AN:

3414

South Asian (SAS)

AF:

0.0271

AC:

414

AN:

15278

European-Finnish (FIN)

AF:

0.0276

AC:

AN:

254

Middle Eastern (MID)

AF:

0.0471

AC:

AN:

1530

European-Non Finnish (NFE)

AF:

0.0217

AC:

15437

AN:

712842

Other (OTH)

AF:

0.0227

AC:

579

AN:

25494

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.463

Heterozygous variant carriers

654

1308

1962

2616

3270

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0224

AC:

3412

AN:

152356

Hom.:

Cov.:

AF XY:

0.0215

AC XY:

1603

AN XY:

74504

show subpopulations

African (AFR)

AF:

0.0234

AC:

972

AN:

41588

American (AMR)

AF:

0.0222

AC:

340

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0372

AC:

129

AN:

3470

East Asian (EAS)

AF:

0.000193

AC:

AN:

5184

South Asian (SAS)

AF:

0.0304

AC:

147

AN:

4830

European-Finnish (FIN)

AF:

0.00828

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0240

AC:

1636

AN:

68038

Other (OTH)

AF:

0.0289

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

178

356

533

711

889

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0140

Hom.:

Bravo

AF:

0.0229

Asia WGS

AF:

0.0120

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

0.57

Mutation Taster

=100/0

polymorphism

(source)

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

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rs16853272

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over