rs11640077

Positions:

• chr16-19513549-A-G
• chr16-19513549-A-T

Variant summary

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

The NM_016641.4(GDE1):​c.438-2605T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,966 control chromosomes in the GnomAD database, including 11,636 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 0.36 (11636 hom., cov: 32)
• Consequence: GDE1 NM_016641.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.18

Genes affected

GDE1 (HGNC:29644): (glycerophosphodiester phosphodiesterase 1) Predicted to enable glycerophosphodiester phosphodiesterase activity; glycerophosphoinositol glycerophosphodiesterase activity; and lysophospholipase activity. Predicted to be involved in N-acylethanolamine metabolic process; ethanolamine metabolic process; and phospholipid metabolic process. Predicted to be located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GDE1	NM_016641.4	c.438-2605T>C		intron_variant		ENST00000353258.8
GDE1	NM_001324066.2	c.108-2605T>C		intron_variant
GDE1	NM_001324067.2	c.438-2605T>C		intron_variant
GDE1	NR_136689.2	n.572-2605T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GDE1	ENST00000353258.8	c.438-2605T>C		intron_variant		1	NM_016641.4	P1
GDE1	ENST00000564172.1	c.*107-2605T>C		intron_variant, NMD_transcript_variant		1
GDE1	ENST00000569773.1	c.108-2605T>C		intron_variant		3
GDE1	ENST00000569899.5	c.156-2605T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55249 AN: 151848 Hom.: 11606 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.364 AC: 55322 AN: 151966 Hom.: 11636 Cov.: 32 AF XY: 0.364 AC XY: 27013 AN XY: 74278

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.320

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.365

Alfa AF: 0.240 Hom.: 836

Bravo AF: 0.396

Asia WGS AF: 0.381 AC: 1325 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.82
DANN	Benign	0.43

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: rs11640077; hg19: chr16-19524871;