chr10-112311590-A-G

Position:

• chr10-112311590-A-G

Variant summary

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

The NR_028134.1(GUCY2GP):​n.2680-337T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 152,040 control chromosomes in the GnomAD database, including 14,119 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 (14119 hom., cov: 32)
• Consequence: GUCY2GP NR_028134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.14

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GUCY2GP	NR_028134.1	n.2680-337T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GUCY2GP	ENST00000479705.5	n.2931-337T>C		intron_variant, non_coding_transcript_variant
	ENST00000638284.2	n.1913-337T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63967 AN: 151922 Hom.: 14115 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.428

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.421 AC: 64010 AN: 152040 Hom.: 14119 Cov.: 32 AF XY: 0.425 AC XY: 31586 AN XY: 74320

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.445

Gnomad4 NFE AF: 0.479

Gnomad4 OTH AF: 0.431

Alfa AF: 0.445 Hom.: 3280

Bravo AF: 0.412

Asia WGS AF: 0.545 AC: 1893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0050
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12414024; hg19: chr10-114071348;