ENST00000564172.1:n.*1316T>C – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000564172.1(GDE1):n.*1316T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 152,178 control chromosomes in the GnomAD database, including 54,753 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 0.85 ( 54747 hom., cov: 31)

Exomes 𝑓: 0.93 ( 6 hom. )

Consequence

GDE1
ENST00000564172.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.549

Publications

19 publications found

Variant links:

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]

GDE1 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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.884 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
GDE1	NM_016641.4 link	c.*651T>C	3_prime_UTR_variant	Exon 6 of 6	ENST00000353258.8	NP_057725.1	Q9NZC3
GDE1	NR_136689.2 link	n.1813T>C	non_coding_transcript_exon_variant	Exon 6 of 6
GDE1	NM_001324067.2 link	c.*651T>C	3_prime_UTR_variant	Exon 5 of 5		NP_001310996.1
GDE1	NM_001324066.2 link	c.*651T>C	3_prime_UTR_variant	Exon 6 of 6		NP_001310995.1	A0A024QYU1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
GDE1	ENST00000564172.1 link	n.*1316T>C	non_coding_transcript_exon_variant	Exon 6 of 6	1		ENSP00000457431.1	H3BU22
GDE1	ENST00000353258.8 link	c.*651T>C	3_prime_UTR_variant	Exon 6 of 6	1	NM_016641.4	ENSP00000261386.3	Q9NZC3
GDE1	ENST00000564172.1 link	n.*1316T>C	3_prime_UTR_variant	Exon 6 of 6	1		ENSP00000457431.1	H3BU22

Frequencies

GnomAD3 genomes

AF:

0.848

AC:

128873

AN:

152046

Hom.:

54695

Cov.:

show subpopulations

Gnomad AFR

AF:

0.838

Gnomad AMI

AF:

0.895

Gnomad AMR

AF:

0.805

Gnomad ASJ

AF:

0.783

Gnomad EAS

AF:

0.834

Gnomad SAS

AF:

0.905

Gnomad FIN

AF:

0.896

Gnomad MID

AF:

0.794

Gnomad NFE

AF:

0.856

Gnomad OTH

AF:

0.827

GnomAD4 exome

AF:

0.929

AC:

AN:

Hom.:

Cov.:

AF XY:

0.917

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.917

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.848

AC:

128980

AN:

152164

Hom.:

54747

Cov.:

AF XY:

0.849

AC XY:

63136

AN XY:

74386

show subpopulations

African (AFR)

AF:

0.838

AC:

34794

AN:

41512

American (AMR)

AF:

0.805

AC:

12295

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.783

AC:

2717

AN:

3470

East Asian (EAS)

AF:

0.833

AC:

4296

AN:

5156

South Asian (SAS)

AF:

0.906

AC:

4374

AN:

4828

European-Finnish (FIN)

AF:

0.896

AC:

9493

AN:

10596

Middle Eastern (MID)

AF:

0.810

AC:

238

AN:

294

European-Non Finnish (NFE)

AF:

0.856

AC:

58205

AN:

68006

Other (OTH)

AF:

0.830

AC:

1752

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1025

2050

3074

4099

5124

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

896

1792

2688

3584

4480

<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:

0.846

Hom.:

137590

Bravo

AF:

0.837

Asia WGS

AF:

0.873

AC:

3036

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

8.6

(source)

DANN

Benign

0.65

PhyloP100

0.55

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over