dbSNP rs2269423: AGPAT1:c.-10+71T>G (chr6-32177930-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0230

Publications

46 publications found

Variant links:

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]

AGPAT1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
AGPAT1	NM_032741.5 link	c.-10+71T>G		intron_variant	Intron 1 of 6		NP_116130.2	Q99943A0A024RCV5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGPAT1	ENST00000336984.6 link	c.-10+71T>G		intron_variant	Intron 1 of 6	1		ENSP00000337463.6		Q99943
AGPAT1	ENST00000395497.5 link	c.-396T>G		upstream_gene_variant		5		ENSP00000378875.1		Q99943

Frequencies

GnomAD3 genomes

AF:

0.650

AC:

98715

AN:

151936

Hom.:

32321

Cov.:

show subpopulations

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.:

Cov.:

AF XY:

0.778

AC XY:

112

AN XY:

144

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.813

AC:

122

AN:

150

European-Finnish (FIN)

AF:

0.667

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.563

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.521

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.650

AC:

98789

AN:

152054

Hom.:

32342

Cov.:

AF XY:

0.649

AC XY:

48263

AN XY:

74322

show subpopulations

African (AFR)

AF:

0.693

AC:

28736

AN:

41480

American (AMR)

AF:

0.637

AC:

9728

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.789

AC:

2738

AN:

3472

East Asian (EAS)

AF:

0.653

AC:

3371

AN:

5166

South Asian (SAS)

AF:

0.741

AC:

3574

AN:

4824

European-Finnish (FIN)

AF:

0.573

AC:

6052

AN:

10558

Middle Eastern (MID)

AF:

0.759

AC:

223

AN:

294

European-Non Finnish (NFE)

AF:

0.622

AC:

42259

AN:

67972

Other (OTH)

AF:

0.696

AC:

1470

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1758

3516

5275

7033

8791

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

802

1604

2406

3208

4010

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.640

Hom.:

124341

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

(source)

DANN

Benign

0.53

PhyloP100

-0.023

PromoterAI

-0.0014

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over