rs17673844

Variant names:

• chr10-112340851-G-C
• rs17673844
• ENST00000479705.5:n.1430C>G

Variant summary

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

The ENST00000638284.2(ENSG00000293449):​n.547C>G 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 0.0434 in 152,272 control chromosomes in the GnomAD database, including 196 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 0.043 (196 hom., cov: 32)
  • Exomes 𝑓: 0.14 (0 hom.)
• Consequence: ENSG00000293449 ENST00000638284.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.910
• 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=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0633 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.1314C>G		non_coding_transcript_exon	Exon 7 of 19

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GUCY2GP	ENST00000479705.5	TSL:6	n.1430C>G		non_coding_transcript_exon	Exon 8 of 21
	ENSG00000293449	ENST00000638284.2	TSL:3	n.547C>G		non_coding_transcript_exon	Exon 5 of 17

Frequencies

GnomAD3 genomes AF: 0.0434 AC: 6610 AN: 152132 Hom.: 196 Cov.: 32

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0377

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0267

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0649

Gnomad OTH AF: 0.0551

GnomAD4 exome AF: 0.136 AC: 3 AN: 22 Hom.: 0 Cov.: 0 AF XY: 0.188 AC XY: 3 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.167 AC: 1 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.143 AC: 2 AN: 14

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.0434 AC: 6607 AN: 152250 Hom.: 196 Cov.: 32 AF XY: 0.0414 AC XY: 3085 AN XY: 74436

African (AFR) AF: 0.0110 AC: 457 AN: 41550

American (AMR) AF: 0.0376 AC: 576 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.0272 AC: 131 AN: 4824

European-Finnish (FIN) AF: 0.0452 AC: 480 AN: 10608

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0649 AC: 4415 AN: 68004

Other (OTH) AF: 0.0540 AC: 114 AN: 2110

Alfa AF: 0.0594 Hom.: 33

Bravo AF: 0.0428

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	7.9
DANN	Benign	0.67
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs17673844; hg19: chr10-114100609;