rs10187256

Positions:

• chr2-68922849-A-G

Variant summary

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

The ENST00000637675.1(GKN3P):​n.176A>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 0.122 in 398,482 control chromosomes in the GnomAD database, including 7,406 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 0.19 (5743 hom., cov: 32)
  • Exomes 𝑓: 0.079 (1663 hom.)
• Consequence: GKN3P ENST00000637675.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.60

Genes affected

GKN3P (HGNC:37701): (gastrokine 3, pseudogene) Predicted to be involved in regulation of cell population proliferation. Predicted to act upstream of or within negative regulation of epithelial cell proliferation. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GKN3P	ENST00000637675.1	n.176A>G		non_coding_transcript_exon_variant	3/6	5

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28863 AN: 152074 Hom.: 5716 Cov.: 32

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.0819

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0315

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.173

GnomAD4 exome AF: 0.0794 AC: 19555 AN: 246290 Hom.: 1663 Cov.: 0 AF XY: 0.0769 AC XY: 9594 AN XY: 124800

Gnomad4 AFR exome AF: 0.504

Gnomad4 AMR exome AF: 0.109

Gnomad4 ASJ exome AF: 0.0859

Gnomad4 EAS exome AF: 0.000131

Gnomad4 SAS exome AF: 0.0290

Gnomad4 FIN exome AF: 0.0378

Gnomad4 NFE exome AF: 0.0712

Gnomad4 OTH exome AF: 0.119

GnomAD4 genome AF: 0.190 AC: 28935 AN: 152192 Hom.: 5743 Cov.: 32 AF XY: 0.184 AC XY: 13694 AN XY: 74426

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0819

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0307

Gnomad4 FIN AF: 0.0331

Gnomad4 NFE AF: 0.0680

Gnomad4 OTH AF: 0.171

Alfa AF: 0.139 Hom.: 439

Bravo AF: 0.214

Asia WGS AF: 0.0500 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10187256; hg19: chr2-69149981;