rs10885330

Positions:

• chr10-112312386-C-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

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 -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	UniProt
GUCY2GP	NR_028134.1	n.2610G>T		non_coding_transcript_exon_variant	16/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GUCY2GP	ENST00000479705.5	n.2861G>T		non_coding_transcript_exon_variant	18/21
	ENST00000638284.2	n.1843G>T		non_coding_transcript_exon_variant	14/17	3

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63839 AN: 151984 Hom.: 14032 Cov.: 33

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: 42 AN: 82 Hom.: 10 Cov.: 0 AF XY: 0.500 AC XY: 29 AN XY: 58

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.: 33 AF XY: 0.423 AC XY: 31453 AN XY: 74356

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

Other links and lift over

dbSNP: rs10885330; hg19: chr10-114072144;