rs1046449

Positions:

• chr8-6758233-G-A
• chr8-6758233-G-C

Variant summary

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

The ENST00000285518.11(AGPAT5):​c.*845G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,650 control chromosomes in the GnomAD database, including 1,883 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 0.15 (1878 hom., cov: 33)
  • Exomes 𝑓: 0.13 (5 hom.)
• Consequence: AGPAT5 ENST00000285518.11 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110

Genes affected

AGPAT5 (HGNC:20886): (1-acylglycerol-3-phosphate O-acyltransferase 5) 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. A pseudogene of this gene is present on the Y chromosome. [provided by RefSeq, Aug 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGPAT5	NM_018361.5	c.*845G>A		3_prime_UTR_variant	8/8	ENST00000285518.11	NP_060831.2
AGPAT5	XM_047421938.1	c.*845G>A		3_prime_UTR_variant	7/7		XP_047277894.1
AGPAT5	XM_047421939.1	c.*845G>A		3_prime_UTR_variant	9/9		XP_047277895.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGPAT5	ENST00000285518.11	c.*845G>A		3_prime_UTR_variant	8/8	1	NM_018361.5	ENSP00000285518	P1
AGPAT5	ENST00000523234.5	c.*1603G>A		3_prime_UTR_variant, NMD_transcript_variant	7/7	5		ENSP00000430016

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22400 AN: 152100 Hom.: 1874 Cov.: 33

Gnomad AFR AF: 0.0949

Gnomad AMI AF: 0.109

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.152

Gnomad OTH AF: 0.165

GnomAD4 exome AF: 0.130 AC: 56 AN: 432 Hom.: 5 Cov.: 0 AF XY: 0.133 AC XY: 35 AN XY: 264

Gnomad4 AMR exome AF: 0.500

Gnomad4 FIN exome AF: 0.128

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.147 AC: 22411 AN: 152218 Hom.: 1878 Cov.: 33 AF XY: 0.150 AC XY: 11163 AN XY: 74426

Gnomad4 AFR AF: 0.0948

Gnomad4 AMR AF: 0.228

Gnomad4 ASJ AF: 0.156

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.235

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.152

Gnomad4 OTH AF: 0.161

Alfa AF: 0.155 Hom.: 3167

Bravo AF: 0.150

Asia WGS AF: 0.177 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.67

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: rs1046449; hg19: chr8-6615754;