rs2277091

Positions:

• chr6-161146301-G-A

Variant summary

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

The NM_020133.3(AGPAT4):​c.843+223C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 150,500 control chromosomes in the GnomAD database, including 9,213 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 0.32 (9213 hom., cov: 31)
• Consequence: AGPAT4 NM_020133.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.381

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]

LOC124901455 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGPAT4	NM_020133.3	c.843+223C>T		intron_variant		ENST00000320285.9
LOC124901455	XR_007059860.1	n.6075G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGPAT4	ENST00000320285.9	c.843+223C>T		intron_variant		1	NM_020133.3	P1
AGPAT4	ENST00000366911.9	c.*316+223C>T		intron_variant		1
AGPAT4	ENST00000437165.1	c.179+223C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.316 AC: 47579 AN: 150396 Hom.: 9214 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.316 AC: 47578 AN: 150500 Hom.: 9213 Cov.: 31 AF XY: 0.318 AC XY: 23389 AN XY: 73580

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.400

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.413

Gnomad4 OTH AF: 0.364

Alfa AF: 0.407 Hom.: 18046

Bravo AF: 0.299

Asia WGS AF: 0.319 AC: 1110 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.6
DANN	Benign	0.77

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: rs2277091; hg19: chr6-161567333;