rs17129583

Positions:

• chr10-112169406-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001244949.2(GPAM):​c.795-454T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,236 control chromosomes in the GnomAD database, including 1,063 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 0.11 (1063 hom., cov: 32)
• Consequence: GPAM NM_001244949.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPAM	NM_001244949.2	c.795-454T>C		intron_variant		ENST00000348367.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPAM	ENST00000348367.9	c.795-454T>C		intron_variant		1	NM_001244949.2	P1
GPAM	ENST00000369425.5	c.795-454T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16707 AN: 152118 Hom.: 1063 Cov.: 32

Gnomad AFR AF: 0.0569

Gnomad AMI AF: 0.0943

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.0619

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.124

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.110 AC: 16714 AN: 152236 Hom.: 1063 Cov.: 32 AF XY: 0.113 AC XY: 8394 AN XY: 74424

Gnomad4 AFR AF: 0.0569

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.0619

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.125

Alfa AF: 0.117 Hom.: 133

Bravo AF: 0.107

Asia WGS AF: 0.204 AC: 706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.74

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

Publications

LitVar

Other links and lift over

dbSNP: rs17129583; hg19: chr10-113929164;