NM_138814.4:c.*504A>G

Variant names:

• chr22-43880291-T-C
• rs470093
• NM_138814.4:c.*504A>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_138814.4(PNPLA5):​c.*504A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 34)
• Consequence: PNPLA5 NM_138814.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330
• Publications: 8 publications found

Genes affected

PNPLA5 (HGNC:24888): (patatin like phospholipase domain containing 5) This gene is a member of the patatin-like phospholipase family; its encoded protein has been shown to inhibit transacylation. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Apr 2010]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138814.4. 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
	PNPLA5	NM_138814.4	MANE Select	c.*504A>G		3_prime_UTR	Exon 9 of 9	NP_620169.1	Q7Z6Z6-1
	PNPLA5	NM_001177675.2		c.*504A>G		3_prime_UTR	Exon 7 of 7	NP_001171146.1	Q7Z6Z6-2
	PNPLA5	NM_001371410.1		c.*504A>G		3_prime_UTR	Exon 9 of 9	NP_001358339.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PNPLA5	ENST00000216177.9	TSL:1 MANE Select	c.*504A>G		3_prime_UTR	Exon 9 of 9	ENSP00000216177.3	Q7Z6Z6-1
	PNPLA5	ENST00000940360.1		c.*504A>G		3_prime_UTR	Exon 8 of 8	ENSP00000610419.1
	PNPLA5	ENST00000940358.1		c.*504A>G		3_prime_UTR	Exon 8 of 8	ENSP00000610417.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.84
PhyloP100		-0.033

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

Other links and lift over

dbSNP: rs470093; hg19: chr22-44276171;