Genetic Variant NM_001244949.2:c.*86A>G (chr10-112153464-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001244949.2(GPAM):c.*86A>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 0.713 in 1,604,694 control chromosomes in the GnomAD database, including 409,275 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 0.69 ( 36006 hom., cov: 30)

Exomes 𝑓: 0.72 ( 373269 hom. )

Consequence

GPAM
NM_001244949.2 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.596

Publications

26 publications found

Variant links:

Genes affected

GPAM (HGNC:24865): (glycerol-3-phosphate acyltransferase, mitochondrial) This gene encodes a mitochondrial enzyme which prefers saturated fatty acids as its substrate for the synthesis of glycerolipids. This metabolic pathway's first step is catalyzed by the encoded enzyme. Two forms for this enzyme exist, one in the mitochondria and one in the endoplasmic reticulum. Two alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Oct 2011]

GPAM links:

ENSG00000295048 (HGNC:):

ENSG00000295048 links:

Genome browser will be placed here

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=-0.62).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.804 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPAM	NM_001244949.2 link	c.*86A>G		3_prime_UTR_variant	Exon 22 of 22	ENST00000348367.9	NP_001231878.1	Q9HCL2Q8N1G6Q86T70

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPAM	ENST00000348367.9 link	c.*86A>G		3_prime_UTR_variant	Exon 22 of 22	1	NM_001244949.2	ENSP00000265276.4		Q9HCL2
ENSG00000295048	ENST00000727646.1 link	n.249-2437T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.688

AC:

104389

AN:

151762

Hom.:

35994

Cov.:

show subpopulations

Gnomad AFR

AF:

0.667

Gnomad AMI

AF:

0.572

Gnomad AMR

AF:

0.676

Gnomad ASJ

AF:

0.578

Gnomad EAS

AF:

0.735

Gnomad SAS

AF:

0.826

Gnomad FIN

AF:

0.643

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.705

Gnomad OTH

AF:

0.673

GnomAD4 exome

AF:

0.716

AC:

1039494

AN:

1452814

Hom.:

373269

Cov.:

AF XY:

0.717

AC XY:

518456

AN XY:

722868

show subpopulations

African (AFR)

AF:

0.671

AC:

22353

AN:

33302

American (AMR)

AF:

0.708

AC:

31529

AN:

44544

Ashkenazi Jewish (ASJ)

AF:

0.567

AC:

14720

AN:

25952

East Asian (EAS)

AF:

0.753

AC:

29707

AN:

39458

South Asian (SAS)

AF:

0.815

AC:

69822

AN:

85624

European-Finnish (FIN)

AF:

0.654

AC:

32753

AN:

50088

Middle Eastern (MID)

AF:

0.653

AC:

3612

AN:

5534

European-Non Finnish (NFE)

AF:

0.715

AC:

792409

AN:

1108382

Other (OTH)

AF:

0.711

AC:

42589

AN:

59930

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

15306

30612

45917

61223

76529

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19944

39888

59832

79776

99720

<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:

0.688

AC:

104441

AN:

151880

Hom.:

36006

Cov.:

AF XY:

0.686

AC XY:

50926

AN XY:

74224

show subpopulations

African (AFR)

AF:

0.666

AC:

27575

AN:

41398

American (AMR)

AF:

0.675

AC:

10289

AN:

15246

Ashkenazi Jewish (ASJ)

AF:

0.578

AC:

2004

AN:

3470

East Asian (EAS)

AF:

0.736

AC:

3768

AN:

5122

South Asian (SAS)

AF:

0.826

AC:

3980

AN:

4820

European-Finnish (FIN)

AF:

0.643

AC:

6788

AN:

10562

Middle Eastern (MID)

AF:

0.592

AC:

173

AN:

292

European-Non Finnish (NFE)

AF:

0.705

AC:

47922

AN:

67954

Other (OTH)

AF:

0.675

AC:

1425

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1633

3266

4900

6533

8166

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

830

1660

2490

3320

4150

<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:

0.695

Hom.:

136999

Bravo

AF:

0.683

Asia WGS

AF:

0.782

AC:

2720

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

4.3

(source)

DANN

Benign

0.76

PhyloP100

-0.60

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

Details are displayed if max score is > 0.2

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