2-68922854-G-A

Position:

• chr2-68922854-G-A

Variant summary

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

The ENST00000637675.1(GKN3P):​n.181G>A 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 0.0575 in 398,476 control chromosomes in the GnomAD database, including 826 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 0.054 (278 hom., cov: 32)
  • Exomes 𝑓: 0.060 (548 hom.)
• Consequence: GKN3P ENST00000637675.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.57

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=-0.48).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0704 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.181G>A		non_coding_transcript_exon_variant	3/6	5

Frequencies

GnomAD3 genomes AF: 0.0542 AC: 8250 AN: 152074 Hom.: 278 Cov.: 32

Gnomad AFR AF: 0.0393

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0741

Gnomad ASJ AF: 0.0810

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0295

Gnomad FIN AF: 0.0329

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0650

Gnomad OTH AF: 0.0752

GnomAD4 exome AF: 0.0595 AC: 14656 AN: 246284 Hom.: 548 Cov.: 0 AF XY: 0.0597 AC XY: 7445 AN XY: 124792

Gnomad4 AFR exome AF: 0.0428

Gnomad4 AMR exome AF: 0.0636

Gnomad4 ASJ exome AF: 0.0855

Gnomad4 EAS exome AF: 0.000131

Gnomad4 SAS exome AF: 0.0284

Gnomad4 FIN exome AF: 0.0373

Gnomad4 NFE exome AF: 0.0688

Gnomad4 OTH exome AF: 0.0696

GnomAD4 genome AF: 0.0541 AC: 8241 AN: 152192 Hom.: 278 Cov.: 32 AF XY: 0.0529 AC XY: 3934 AN XY: 74406

Gnomad4 AFR AF: 0.0391

Gnomad4 AMR AF: 0.0740

Gnomad4 ASJ AF: 0.0810

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0291

Gnomad4 FIN AF: 0.0329

Gnomad4 NFE AF: 0.0649

Gnomad4 OTH AF: 0.0739

Alfa AF: 0.0573 Hom.: 40

Bravo AF: 0.0588

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	16
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs75578132; hg19: chr2-69149986;