rs2269423

Positions:

• chr6-32177930-A-C
• chr6-32177930-A-G
• chr6-32177930-A-T

Variant summary

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

The ENST00000336984.6(AGPAT1):​c.-10+71T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 152,228 control chromosomes in the GnomAD database, including 32,397 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 0.65 (32342 hom., cov: 31)
  • Exomes 𝑓: 0.78 (55 hom.)
• Consequence: AGPAT1 ENST00000336984.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0230

Genes affected

AGPAT1 (HGNC:324): (1-acylglycerol-3-phosphate O-acyltransferase 1) This gene encodes an enzyme that converts lysophosphatidic acid (LPA) into phosphatidic acid (PA). LPA and PA are two phospholipids involved in signal transduction and in lipid biosynthesis in cells. This enzyme localizes to the endoplasmic reticulum. This gene is located in the class III region of the human major histocompatibility complex. Alternative splicing results in two transcript variants encoding the same protein. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.721 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGPAT1	NM_032741.5	c.-10+71T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGPAT1	ENST00000336984.6	c.-10+71T>G		intron_variant		1		P1

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98715 AN: 151936 Hom.: 32321 Cov.: 31

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.637

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.695

GnomAD4 exome AF: 0.776 AC: 135 AN: 174 Hom.: 55 Cov.: 0 AF XY: 0.778 AC XY: 112 AN XY: 144

Gnomad4 SAS exome AF: 0.813

Gnomad4 FIN exome AF: 0.667

Gnomad4 NFE exome AF: 0.563

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.650 AC: 98789 AN: 152054 Hom.: 32342 Cov.: 31 AF XY: 0.649 AC XY: 48263 AN XY: 74322

Gnomad4 AFR AF: 0.693

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.653

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.696

Alfa AF: 0.641 Hom.: 52500

Bravo AF: 0.657

Asia WGS AF: 0.714 AC: 2485 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.9
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2269423; hg19: chr6-32145707;