ENST00000416713.5:c.-114+3313G>A

Variant names:

• chr2-28460510-G-A
• rs10209501
• ENST00000416713.5:c.-114+3313G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 1 publications found

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]

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

ACMG classification

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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLB1	ENST00000416713.5	TSL:5	c.-114+3313G>A		intron	N/A	ENSP00000407076.1
	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.: 32

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

African (AFR) AF: 0.0808 AC: 16 AN: 198

American (AMR) AF: 0.147 AC: 94 AN: 638

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 96 AN: 346

East Asian (EAS) AF: 0.114 AC: 49 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: 17 AN: 54

European-Non Finnish (NFE) AF: 0.257 AC: 2450 AN: 9524

Other (OTH) AF: 0.247 AC: 219 AN: 888

GnomAD4 genome AF: 0.255 AC: 38732 AN: 152036 Hom.: 5560 Cov.: 32 AF XY: 0.252 AC XY: 18760 AN XY: 74328

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

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
DANN	Benign	0.33
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10209501; hg19: chr2-28683377;