Variant 10-112312386-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NR_028134.1(GUCY2GP):n.2610G>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
NR_028134.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0320

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
GUCY2GP	NR_028134.1 link	n.2610G>T		non_coding_transcript_exon_variant	16/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GUCY2GP	ENST00000479705.5 link	n.2861G>T		non_coding_transcript_exon_variant	18/21	6
GUCY2GP	ENST00000490269.1 link	n.1077G>T		non_coding_transcript_exon_variant	8/11	5

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

Gnomad4 AFR exome

AF:

0.167

Gnomad4 AMR exome

AF:

1.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.250

Gnomad4 SAS exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.533

Gnomad4 OTH exome

AF:

0.750

GnomAD4 genome

AF:

0.420

AC:

63884

AN:

152102

Hom.:

14036

Cov.:

AF XY:

0.423

AC XY:

31453

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.278

Gnomad4 AMR

AF:

0.474

Gnomad4 ASJ

AF:

0.350

Gnomad4 EAS

AF:

0.500

Gnomad4 SAS

AF:

0.510

Gnomad4 FIN

AF:

0.445

Gnomad4 NFE

AF:

0.479

Gnomad4 OTH

AF:

0.430

Alfa

AF:

0.458

Hom.:

12527

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

DANN

Benign

0.80

Splicing

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