dbSNP rs10885330: GUCY2GP:n.2861G>T (chr10-112312386-C-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000479705.5(GUCY2GP):n.2861G>T 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 0.42 in 152,184 control chromosomes in the GnomAD database, including 14,046 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 0.42 ( 14036 hom., cov: 33)

Exomes 𝑓: 0.51 ( 10 hom. )

Consequence

GUCY2GP
ENST00000479705.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0320

Publications

6 publications found

Variant links:

Genes affected

GUCY2GP (HGNC:31863): (guanylate cyclase 2G, pseudogene) Predicted to enable guanylate cyclase activity. Predicted to be located in external side of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

GUCY2GP links:

ENSG00000293449 (HGNC:):

ENSG00000293449 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.27).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GUCY2GP	NR_028134.1 link	n.2610G>T		non_coding_transcript_exon_variant	Exon 16 of 19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GUCY2GP	ENST00000479705.5 link	n.2861G>T		non_coding_transcript_exon_variant	Exon 18 of 21	6
ENSG00000293449	ENST00000638284.2 link	n.1843G>T		non_coding_transcript_exon_variant	Exon 14 of 17	3

Frequencies

GnomAD3 genomes

AF:

0.420

AC:

63839

AN:

151984

Hom.:

14032

Cov.:

show subpopulations

Gnomad AFR

AF:

0.278

Gnomad AMI

AF:

0.567

Gnomad AMR

AF:

0.474

Gnomad ASJ

AF:

0.350

Gnomad EAS

AF:

0.499

Gnomad SAS

AF:

0.508

Gnomad FIN

AF:

0.445

Gnomad MID

AF:

0.462

Gnomad NFE

AF:

0.479

Gnomad OTH

AF:

0.426

GnomAD4 exome

AF:

0.512

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.167

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.250

AC:

AN:

South Asian (SAS)

AF:

0.500

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.533

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.420

AC:

63884

AN:

152102

Hom.:

14036

Cov.:

AF XY:

0.423

AC XY:

31453

AN XY:

74356

show subpopulations

African (AFR)

AF:

0.278

AC:

11555

AN:

41510

American (AMR)

AF:

0.474

AC:

7244

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.350

AC:

1214

AN:

3470

East Asian (EAS)

AF:

0.500

AC:

2572

AN:

5146

South Asian (SAS)

AF:

0.510

AC:

2461

AN:

4828

European-Finnish (FIN)

AF:

0.445

AC:

4706

AN:

10572

Middle Eastern (MID)

AF:

0.469

AC:

138

AN:

294

European-Non Finnish (NFE)

AF:

0.479

AC:

32570

AN:

67964

Other (OTH)

AF:

0.430

AC:

908

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1871

3742

5613

7484

9355

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

614

1228

1842

2456

3070

<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:

0.455

Hom.:

16738

Bravo

AF:

0.412

Asia WGS

AF:

0.525

AC:

1826

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.27

CADD

Benign

7.5

(source)

DANN

Benign

0.80

PhyloP100

-0.032

Splicing

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