dbSNP rs10209501: PLB1:c.-114+3313G>A (chr2-28460510-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000416713.5(PLB1):c.-114+3313G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 167,216 control chromosomes in the GnomAD database, including 6,097 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 0.25 ( 5560 hom., cov: 32)

Exomes 𝑓: 0.24 ( 537 hom. )

Consequence

PLB1
ENST00000416713.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.64

Publications

1 publications found

Variant links:

Genes affected

PLB1 (HGNC:30041): (phospholipase B1) This gene encodes a membrane-associated phospholipase that displays lysophospholipase and phospholipase A2 activities through removal of sn-1 and sn-2 fatty acids of glycerophospholipids. In addition, it displays lipase and retinyl ester hydrolase activities. The encoded protein is highly conserved and is composed of a large, glycosylated extracellular domain composed of four tandem homologous domains, followed by a hydrophobic segment that anchors the enzyme to the membrane and a short C-terminal cytoplasmic tail. This gene has been identified as a candidate rheumatoid arthritis risk gene. [provided by RefSeq, Jul 2016]

PLB1 links:

SNRPGP7 (HGNC:39326): (small nuclear ribonucleoprotein polypeptide G pseudogene 7)

SNRPGP7 links:

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new If you want to explore the variant's impact on the transcript ENST00000416713.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.99).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000416713.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLB1	ENST00000416713.5	TSL:5	c.-114+3313G>A		intron	N/A	ENSP00000407076.1	C9JYQ2
	SNRPGP7	ENST00000469016.1	TSL:6	n.-149C>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38735

AN:

151918

Hom.:

5566

Cov.:

show subpopulations

Gnomad AFR

AF:

0.127

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.378

Gnomad EAS

AF:

0.161

Gnomad SAS

AF:

0.337

Gnomad FIN

AF:

0.265

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.328

Gnomad OTH

AF:

0.278

GnomAD4 exome

AF:

0.243

AC:

3692

AN:

15180

Hom.:

537

AF XY:

0.243

AC XY:

2050

AN XY:

8442

show subpopulations

African (AFR)

AF:

0.0808

AC:

AN:

198

American (AMR)

AF:

0.147

AC:

AN:

638

Ashkenazi Jewish (ASJ)

AF:

0.277

AC:

AN:

346

East Asian (EAS)

AF:

0.114

AC:

AN:

430

South Asian (SAS)

AF:

0.248

AC:

611

AN:

2468

European-Finnish (FIN)

AF:

0.221

AC:

140

AN:

634

Middle Eastern (MID)

AF:

0.315

AC:

AN:

European-Non Finnish (NFE)

AF:

0.257

AC:

2450

AN:

9524

Other (OTH)

AF:

0.247

AC:

219

AN:

888

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

137

274

412

549

686

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.255

AC:

38732

AN:

152036

Hom.:

5560

Cov.:

AF XY:

0.252

AC XY:

18760

AN XY:

74328

show subpopulations

African (AFR)

AF:

0.127

AC:

5265

AN:

41468

American (AMR)

AF:

0.236

AC:

3605

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.378

AC:

1313

AN:

3470

East Asian (EAS)

AF:

0.161

AC:

832

AN:

5174

South Asian (SAS)

AF:

0.337

AC:

1620

AN:

4814

European-Finnish (FIN)

AF:

0.265

AC:

2802

AN:

10560

Middle Eastern (MID)

AF:

0.374

AC:

110

AN:

294

European-Non Finnish (NFE)

AF:

0.328

AC:

22318

AN:

67970

Other (OTH)

AF:

0.273

AC:

577

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1457

2915

4372

5830

7287

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

414

828

1242

1656

2070

<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:

0.288

Hom.:

908

Bravo

AF:

0.241

Asia WGS

AF:

0.232

AC:

807

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.68

(source)

DANN

Benign

0.33

PhyloP100

-1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over