rs7435

Positions:

• chr21-43984457-A-G

Variant summary

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

The NM_020132.5(AGPAT3):​c.*2065A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,588 control chromosomes in the GnomAD database, including 9,806 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 0.35 (9785 hom., cov: 32)
  • Exomes 𝑓: 0.28 (21 hom.)
• Consequence: AGPAT3 NM_020132.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

Genes affected

AGPAT3 (HGNC:326): (1-acylglycerol-3-phosphate O-acyltransferase 3) The protein encoded by this gene is an acyltransferase that converts lysophosphatidic acid into phosphatidic acid, which is the second step in the de novo phospholipid biosynthetic pathway. The encoded protein may be an integral membrane protein. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGPAT3	NM_020132.5	c.*2065A>G		3_prime_UTR_variant	10/10	ENST00000291572.13	NP_064517.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGPAT3	ENST00000291572.13	c.*2065A>G		3_prime_UTR_variant	10/10	1	NM_020132.5	ENSP00000291572.8

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53730 AN: 152010 Hom.: 9739 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.367

GnomAD4 exome AF: 0.283 AC: 130 AN: 460 Hom.: 21 Cov.: 0 AF XY: 0.294 AC XY: 73 AN XY: 248

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.100

Gnomad4 ASJ exome AF: 0.250

Gnomad4 SAS exome AF: 0.625

Gnomad4 FIN exome AF: 0.299

Gnomad4 NFE exome AF: 0.264

Gnomad4 OTH exome AF: 0.214

GnomAD4 genome AF: 0.354 AC: 53833 AN: 152128 Hom.: 9785 Cov.: 32 AF XY: 0.354 AC XY: 26335 AN XY: 74374

Gnomad4 AFR AF: 0.433

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.373

Alfa AF: 0.326 Hom.: 14114

Bravo AF: 0.366

Asia WGS AF: 0.400 AC: 1389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.7
DANN	Benign	0.58

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

Publications

LitVar

Other links and lift over

dbSNP: rs7435; hg19: chr21-45404338;