rs3798943

Positions:

• chr6-161254459-T-C

Variant summary

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

The NM_020133.3(AGPAT4):​c.-90+19479A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,124 control chromosomes in the GnomAD database, including 20,480 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 0.51 (20480 hom., cov: 33)
• Consequence: AGPAT4 NM_020133.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.577

Genes affected

AGPAT4 (HGNC:20885): (1-acylglycerol-3-phosphate O-acyltransferase 4) This gene encodes a member of the 1-acylglycerol-3-phosphate O-acyltransferase family. This integral membrane protein converts lysophosphatidic acid to phosphatidic acid, the second step in de novo phospholipid biosynthesis. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGPAT4	NM_020133.3	c.-90+19479A>G		intron_variant		ENST00000320285.9	NP_064518.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGPAT4	ENST00000320285.9	c.-90+19479A>G		intron_variant		1	NM_020133.3	ENSP00000314036	P1
AGPAT4	ENST00000366911.9	c.-90+19479A>G		intron_variant		1		ENSP00000355878
AGPAT4	ENST00000366905.3	c.-90+19479A>G		intron_variant		2		ENSP00000355872
AGPAT4	ENST00000624499.2	n.26+19479A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78270 AN: 152006 Hom.: 20456 Cov.: 33

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.528

Gnomad OTH AF: 0.543

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

GnomAD4 genome AF: 0.515 AC: 78339 AN: 152124 Hom.: 20480 Cov.: 33 AF XY: 0.513 AC XY: 38162 AN XY: 74388

Gnomad4 AFR AF: 0.464

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.528

Gnomad4 OTH AF: 0.545

Alfa AF: 0.536 Hom.: 30084

Bravo AF: 0.526

Asia WGS AF: 0.502 AC: 1745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.33
DANN	Benign	0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3798943; hg19: chr6-161675491;