rs10187256

Variant names:

• chr2-68922849-A-G
• rs10187256
• ENST00000637675.1:n.176A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

ENSG00000307469 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637675.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GKN3P	ENST00000637675.1	TSL:5	n.176A>G		non_coding_transcript_exon	Exon 3 of 6
	ENSG00000307469	ENST00000826466.1		n.96+8562T>C		intron	N/A

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

African (AFR) AF: 0.504 AC: 3620 AN: 7180

American (AMR) AF: 0.109 AC: 814 AN: 7434

Ashkenazi Jewish (ASJ) AF: 0.0859 AC: 794 AN: 9240

East Asian (EAS) AF: 0.000131 AC: 3 AN: 22894

South Asian (SAS) AF: 0.0290 AC: 88 AN: 3032

European-Finnish (FIN) AF: 0.0378 AC: 787 AN: 20824

Middle Eastern (MID) AF: 0.192 AC: 249 AN: 1294

European-Non Finnish (NFE) AF: 0.0712 AC: 11256 AN: 158022

Other (OTH) AF: 0.119 AC: 1944 AN: 16370

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

African (AFR) AF: 0.506 AC: 20953 AN: 41450

American (AMR) AF: 0.134 AC: 2052 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0819 AC: 284 AN: 3468

East Asian (EAS) AF: 0.000385 AC: 2 AN: 5192

South Asian (SAS) AF: 0.0307 AC: 148 AN: 4828

European-Finnish (FIN) AF: 0.0331 AC: 351 AN: 10620

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.0680 AC: 4625 AN: 68020

Other (OTH) AF: 0.171 AC: 361 AN: 2112

Alfa AF: 0.154 Hom.: 542

Bravo AF: 0.214

Asia WGS AF: 0.0500 AC: 173 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	15
DANN	Benign	0.44
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs10187256; hg19: chr2-69149981;