rs1046449

Variant names:

• chr8-6758233-G-A
• rs1046449
• NM_018361.5:c.*845G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-6758233-G-A
• chr8-6758233-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018361.5(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 NM_018361.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 5 publications found

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]

AGPAT5 Gene-Disease associations (from GenCC):

• Tourette syndrome

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018361.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGPAT5	NM_018361.5	MANE Select	c.*845G>A		3_prime_UTR	Exon 8 of 8	NP_060831.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGPAT5	ENST00000285518.11	TSL:1 MANE Select	c.*845G>A		3_prime_UTR	Exon 8 of 8	ENSP00000285518.6
	AGPAT5	ENST00000523234.5	TSL:5	n.*1603G>A		non_coding_transcript_exon	Exon 7 of 7	ENSP00000430016.1
	AGPAT5	ENST00000523234.5	TSL:5	n.*1603G>A		3_prime_UTR	Exon 7 of 7	ENSP00000430016.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.500 AC: 1 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.128 AC: 54 AN: 422

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 1 AN: 4

Other (OTH) AF: 0.00 AC: 0 AN: 4

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

African (AFR) AF: 0.0948 AC: 3939 AN: 41552

American (AMR) AF: 0.228 AC: 3492 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 539 AN: 3466

East Asian (EAS) AF: 0.190 AC: 980 AN: 5170

South Asian (SAS) AF: 0.235 AC: 1132 AN: 4820

European-Finnish (FIN) AF: 0.144 AC: 1531 AN: 10596

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.152 AC: 10313 AN: 68002

Other (OTH) AF: 0.161 AC: 340 AN: 2112

Alfa AF: 0.155 Hom.: 5193

Bravo AF: 0.150

Asia WGS AF: 0.177 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.3
DANN	Benign	0.67
PhyloP100		-0.11
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: rs1046449; hg19: chr8-6615754;