rs7925131

Variant names:

• chr11-820268-A-G
• rs7925131
• NM_020376.4:c.187+363A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-820268-A-G
• chr11-820268-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020376.4(PNPLA2):​c.187+363A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,178 control chromosomes in the GnomAD database, including 38,548 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 0.71 (38548 hom., cov: 34)
• Consequence: PNPLA2 NM_020376.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229

Genes affected

PNPLA2 (HGNC:30802): (patatin like phospholipase domain containing 2) This gene encodes an enzyme which catalyzes the first step in the hydrolysis of triglycerides in adipose tissue. Mutations in this gene are associated with neutral lipid storage disease with myopathy. [provided by RefSeq, Jul 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PNPLA2	NM_020376.4	c.187+363A>G		intron_variant	Intron 2 of 9	ENST00000336615.9	NP_065109.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PNPLA2	ENST00000336615.9	c.187+363A>G		intron_variant	Intron 2 of 9	1	NM_020376.4	ENSP00000337701.4

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107679 AN: 152060 Hom.: 38486 Cov.: 34

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.683

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.708 AC: 107798 AN: 152178 Hom.: 38548 Cov.: 34 AF XY: 0.702 AC XY: 52262 AN XY: 74404

Gnomad4 AFR AF: 0.718

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.534

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.502

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.687

Alfa AF: 0.726 Hom.: 11948

Bravo AF: 0.710

Asia WGS AF: 0.598 AC: 2080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	17
DANN	Benign	0.73
RBP_binding_hub_radar		0.77
RBP_regulation_power_radar		1.9

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		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

Other links and lift over

dbSNP: rs7925131; hg19: chr11-820268;