chr6-161146301-G-A

Variant names:

• chr6-161146301-G-A
• rs2277091
• NM_020133.3:c.843+223C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
AGPAT4	NM_020133.3	c.843+223C>T		intron_variant	Intron 7 of 8	ENST00000320285.9	NP_064518.1
LOC124901455	XR_007059860.1	n.6075G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGPAT4	ENST00000320285.9	c.843+223C>T		intron_variant	Intron 7 of 8	1	NM_020133.3	ENSP00000314036.4
AGPAT4	ENST00000366911.9	c.*316+223C>T		intron_variant	Intron 6 of 7	1		ENSP00000355878.5
AGPAT4	ENST00000437165.1	c.177+223C>T		intron_variant	Intron 2 of 2	5		ENSP00000400211.1

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

African (AFR) AF: 0.110 AC: 4394 AN: 40082

American (AMR) AF: 0.318 AC: 4835 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1886 AN: 3462

East Asian (EAS) AF: 0.185 AC: 953 AN: 5154

South Asian (SAS) AF: 0.400 AC: 1916 AN: 4790

European-Finnish (FIN) AF: 0.395 AC: 4175 AN: 10572

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28083 AN: 67934

Other (OTH) AF: 0.364 AC: 761 AN: 2090

Alfa AF: 0.378 Hom.: 23577

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
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2277091; hg19: chr6-161567333;