chr10-112312386-C-A

Variant names:

• chr10-112312386-C-A
• rs10885330
• ENST00000479705.5:n.2861G>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000638284.2(ENSG00000293449):​n.1843G>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: ENSG00000293449 ENST00000638284.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 6 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 -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.

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.2610G>T		non_coding_transcript_exon	Exon 16 of 19

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GUCY2GP	ENST00000479705.5	TSL:6	n.2861G>T		non_coding_transcript_exon	Exon 18 of 21
	ENSG00000293449	ENST00000638284.2	TSL:3	n.1843G>T		non_coding_transcript_exon	Exon 14 of 17

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

African (AFR) AF: 0.167 AC: 1 AN: 6

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.533 AC: 32 AN: 60

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.420 AC: 63884 AN: 152102 Hom.: 14036 Cov.: 33 AF XY: 0.423 AC XY: 31453 AN XY: 74356

African (AFR) AF: 0.278 AC: 11555 AN: 41510

American (AMR) AF: 0.474 AC: 7244 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1214 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2572 AN: 5146

South Asian (SAS) AF: 0.510 AC: 2461 AN: 4828

European-Finnish (FIN) AF: 0.445 AC: 4706 AN: 10572

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

European-Non Finnish (NFE) AF: 0.479 AC: 32570 AN: 67964

Other (OTH) AF: 0.430 AC: 908 AN: 2114

Alfa AF: 0.455 Hom.: 16738

Bravo AF: 0.412

Asia WGS AF: 0.525 AC: 1826 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.27
CADD	Benign	7.5
DANN	Benign	0.80
PhyloP100		-0.032

Splicing

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

Other links and lift over

dbSNP: rs10885330; hg19: chr10-114072144;