10-112311590-A-G

Variant names:

• chr10-112311590-A-G
• rs12414024
• ENST00000479705.5:n.2931-337T>C

Variant summary

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

The ENST00000638284.2(ENSG00000293449):​n.1913-337T>C variant causes a intron 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: ENSG00000293449 ENST00000638284.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.14
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000638284.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GUCY2GP	NR_028134.1		n.2680-337T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GUCY2GP	ENST00000479705.5	TSL:6	n.2931-337T>C		intron	N/A
	ENSG00000293449	ENST00000638284.2	TSL:3	n.1913-337T>C		intron	N/A

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

African (AFR) AF: 0.278 AC: 11523 AN: 41494

American (AMR) AF: 0.474 AC: 7235 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1215 AN: 3472

East Asian (EAS) AF: 0.499 AC: 2577 AN: 5162

South Asian (SAS) AF: 0.547 AC: 2632 AN: 4814

European-Finnish (FIN) AF: 0.445 AC: 4694 AN: 10552

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32567 AN: 67948

Other (OTH) AF: 0.431 AC: 911 AN: 2114

Alfa AF: 0.448 Hom.: 5976

Bravo AF: 0.412

Asia WGS AF: 0.545 AC: 1893 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0050
DANN	Benign	0.29
PhyloP100		-4.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12414024;

hg19: chr10-114071348;