chr10-112319146-G-A

Position:

• chr10-112319146-G-A

Variant summary

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

The NR_028134.1(GUCY2GP):​n.1994-1090C>T 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 0.071 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 NR_028134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252

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=-0.8).
• 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/exons	MANE	Protein	UniProt
GUCY2GP	NR_028134.1	n.1994-1090C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GUCY2GP	ENST00000479705.5	n.2245-1090C>T		intron_variant, non_coding_transcript_variant
	ENST00000638284.2	n.1227-1090C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.0279

Gnomad4 AMR AF: 0.0910

Gnomad4 ASJ AF: 0.0770

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.0973

Gnomad4 FIN AF: 0.0642

Gnomad4 NFE AF: 0.0831

Gnomad4 OTH AF: 0.0834

Alfa AF: 0.0728 Hom.: 53

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11195893; hg19: chr10-114078904;