10-112319146-G-A

Variant names:

• chr10-112319146-G-A
• rs11195893
• ENST00000479705.5:n.2245-1090C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000479705.5(GUCY2GP):​n.2245-1090C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.071 in 152,220 control chromosomes in the GnomAD database, including 511 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 0.071 (511 hom., cov: 32)
• Consequence: GUCY2GP ENST00000479705.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 3 publications found

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]

ENSG00000293449 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GUCY2GP	NR_028134.1	n.1994-1090C>T		intron_variant	Intron 12 of 18

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GUCY2GP	ENST00000479705.5	n.2245-1090C>T		intron_variant	Intron 14 of 20	6
ENSG00000293449	ENST00000638284.2	n.1227-1090C>T		intron_variant	Intron 10 of 16	3

Frequencies

GnomAD3 genomes AF: 0.0710 AC: 10798 AN: 152102 Hom.: 509 Cov.: 32

Gnomad AFR AF: 0.0278

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0904

Gnomad ASJ AF: 0.0770

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.0975

Gnomad FIN AF: 0.0642

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.0829

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

GnomAD4 genome AF: 0.0710 AC: 10813 AN: 152220 Hom.: 511 Cov.: 32 AF XY: 0.0727 AC XY: 5407 AN XY: 74416

African (AFR) AF: 0.0279 AC: 1160 AN: 41532

American (AMR) AF: 0.0910 AC: 1393 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0770 AC: 267 AN: 3468

East Asian (EAS) AF: 0.185 AC: 954 AN: 5170

South Asian (SAS) AF: 0.0973 AC: 470 AN: 4828

European-Finnish (FIN) AF: 0.0642 AC: 680 AN: 10592

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0831 AC: 5649 AN: 68012

Other (OTH) AF: 0.0834 AC: 176 AN: 2110

Alfa AF: 0.0714 Hom.: 54

Bravo AF: 0.0694

Asia WGS AF: 0.116 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.5
DANN	Benign	0.67
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs11195893; hg19: chr10-114078904;