rs7435

Variant names:

• chr21-43984457-A-G
• rs7435
• NM_020132.5:c.*2065A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
AGPAT3	NM_020132.5	c.*2065A>G		3_prime_UTR_variant	Exon 10 of 10	ENST00000291572.13	NP_064517.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGPAT3	ENST00000291572.13	c.*2065A>G		3_prime_UTR_variant	Exon 10 of 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

African (AFR) AF: 0.500 AC: 4 AN: 8

American (AMR) AF: 0.100 AC: 1 AN: 10

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.625 AC: 5 AN: 8

European-Finnish (FIN) AF: 0.299 AC: 40 AN: 134

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.264 AC: 74 AN: 280

Other (OTH) AF: 0.214 AC: 3 AN: 14

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

African (AFR) AF: 0.433 AC: 17959 AN: 41480

American (AMR) AF: 0.391 AC: 5984 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1362 AN: 3468

East Asian (EAS) AF: 0.255 AC: 1318 AN: 5178

South Asian (SAS) AF: 0.388 AC: 1874 AN: 4824

European-Finnish (FIN) AF: 0.276 AC: 2918 AN: 10582

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.312 AC: 21224 AN: 67980

Other (OTH) AF: 0.373 AC: 789 AN: 2116

Alfa AF: 0.332 Hom.: 25824

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
PhyloP100		0.20
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: rs7435; hg19: chr21-45404338;