Genetic Variant GPAM:p.Glu131Gly (chr10-112175621-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001244949.2(GPAM):c.392A>G(p.Glu131Gly) variant causes a missense change. The variant allele was found at a frequency of 0.59 in 1,599,440 control chromosomes in the GnomAD database, including 280,251 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.55 ( 23494 hom., cov: 32)

Exomes 𝑓: 0.59 ( 256757 hom. )

Consequence

GPAM
NM_001244949.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.11

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=4.5096874E-4).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPAM	NM_001244949.2 link	c.392A>G	p.Glu131Gly	missense_variant	Exon 6 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.392A>G	p.Glu131Gly	missense_variant	Exon 6 of 22	1	NM_001244949.2	ENSP00000265276.4		Q9HCL2
GPAM	ENST00000369425.5 link	c.392A>G	p.Glu131Gly	missense_variant	Exon 6 of 19	1		ENSP00000358433.1		Q5VW52

Frequencies

GnomAD3 genomes

AF:

0.553

AC:

84000

AN:

151862

Hom.:

23483

Cov.:

show subpopulations

Gnomad AFR

AF:

0.508

Gnomad AMI

AF:

0.478

Gnomad AMR

AF:

0.498

Gnomad ASJ

AF:

0.518

Gnomad EAS

AF:

0.593

Gnomad SAS

AF:

0.629

Gnomad FIN

AF:

0.515

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.594

Gnomad OTH

AF:

0.535

GnomAD3 exomes

AF:

0.563

AC:

141463

AN:

251388

Hom.:

40124

AF XY:

0.566

AC XY:

76875

AN XY:

135856

show subpopulations

Gnomad AFR exome

AF:

0.506

Gnomad AMR exome

AF:

0.491

Gnomad ASJ exome

AF:

0.515

Gnomad EAS exome

AF:

0.578

Gnomad SAS exome

AF:

0.619

Gnomad FIN exome

AF:

0.525

Gnomad NFE exome

AF:

0.586

Gnomad OTH exome

AF:

0.569

GnomAD4 exome

AF:

0.594

AC:

859349

AN:

1447460

Hom.:

256757

Cov.:

AF XY:

0.594

AC XY:

428069

AN XY:

721044

show subpopulations

Gnomad4 AFR exome

AF:

0.509

Gnomad4 AMR exome

AF:

0.490

Gnomad4 ASJ exome

AF:

0.508

Gnomad4 EAS exome

AF:

0.616

Gnomad4 SAS exome

AF:

0.613

Gnomad4 FIN exome

AF:

0.526

Gnomad4 NFE exome

AF:

0.605

Gnomad4 OTH exome

AF:

0.581

GnomAD4 genome

AF:

0.553

AC:

84045

AN:

151980

Hom.:

23494

Cov.:

AF XY:

0.550

AC XY:

40820

AN XY:

74272

show subpopulations

Gnomad4 AFR

AF:

0.507

Gnomad4 AMR

AF:

0.498

Gnomad4 ASJ

AF:

0.518

Gnomad4 EAS

AF:

0.593

Gnomad4 SAS

AF:

0.629

Gnomad4 FIN

AF:

0.515

Gnomad4 NFE

AF:

0.594

Gnomad4 OTH

AF:

0.538

Alfa

AF:

0.578

Hom.:

54939

Bravo

AF:

0.545

TwinsUK

AF:

0.621

AC:

2303

ALSPAC

AF:

0.609

AC:

2346

ESP6500AA

AF:

0.504

AC:

2220

ESP6500EA

AF:

0.588

AC:

5054

ExAC

AF:

0.566

AC:

68773

Asia WGS

AF:

0.575

AC:

2003

AN:

3478

EpiCase

AF:

0.588

EpiControl

AF:

0.572

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.52

BayesDel_noAF

Benign

-0.37

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.35

T;.

Eigen

Benign

0.18

Eigen_PC

Uncertain

0.28

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.93

D;D

MetaRNN

Benign

0.00045

T;T

MetaSVM

Benign

-0.90

MutationAssessor

Benign

1.7

L;.

PrimateAI

Uncertain

0.58

PROVEAN

Uncertain

-3.3

D;D

REVEL

Benign

0.20

Sift

Uncertain

0.0060

D;D

Sift4G

Uncertain

0.011

D;D

Polyphen

0.25

B;P

Vest4

0.23

MPC

0.44

ClinPred

0.010

GERP RS

5.1

Varity_R

0.35

gMVP

0.47

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over