10-112351785-C-T

Variant summary

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

The NR_028134.1(GUCY2GP):n.778G>A 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 0.631 in 151,962 control chromosomes in the GnomAD database, including 30,591 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 0.63 (30588 hom., cov: 32)
  • Exomes 𝑓: 0.56 (3 hom.)
• Consequence: GUCY2GP NR_028134.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GUCY2GP	NR_028134.1	n.778G>A		non_coding_transcript_exon_variant	3/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GUCY2GP	ENST00000479705.5	n.757G>A		non_coding_transcript_exon_variant	3/21
	ENST00000638284.2	n.11G>A		non_coding_transcript_exon_variant	1/17	3

Frequencies

GnomAD3 genomes AF: 0.631 AC: 95834 AN: 151824 Hom.: 30556 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.663

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.631

GnomAD4 exome AF: 0.563 AC: 9 AN: 16 Hom.: 3 Cov.: 0 AF XY: 0.500 AC XY: 7 AN XY: 14

Gnomad4 NFE exome AF: 0.571

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.631 AC: 95913 AN: 151946 Hom.: 30588 Cov.: 32 AF XY: 0.637 AC XY: 47276 AN XY: 74250

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.633

Alfa AF: 0.644 Hom.: 33902

Bravo AF: 0.625

Asia WGS AF: 0.762 AC: 2650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
Cadd	Benign	1.2
Dann	Benign	0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2148493; hg19: chr10-114111543;