ENST00000637675.1:n.181G>A

Variant names:

• chr2-68922854-G-A
• rs75578132
• ENST00000637675.1:n.181G>A

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.48).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0704 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GKN3P	ENST00000637675.1	TSL:5	n.181G>A		non_coding_transcript_exon	Exon 3 of 6
	ENSG00000307469	ENST00000826466.1		n.96+8557C>T		intron	N/A

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

African (AFR) AF: 0.0428 AC: 307 AN: 7180

American (AMR) AF: 0.0636 AC: 473 AN: 7434

Ashkenazi Jewish (ASJ) AF: 0.0855 AC: 790 AN: 9240

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

South Asian (SAS) AF: 0.0284 AC: 86 AN: 3030

European-Finnish (FIN) AF: 0.0373 AC: 777 AN: 20824

Middle Eastern (MID) AF: 0.167 AC: 216 AN: 1294

European-Non Finnish (NFE) AF: 0.0688 AC: 10865 AN: 158018

Other (OTH) AF: 0.0696 AC: 1139 AN: 16370

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

African (AFR) AF: 0.0391 AC: 1626 AN: 41534

American (AMR) AF: 0.0740 AC: 1132 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0810 AC: 281 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0291 AC: 140 AN: 4812

European-Finnish (FIN) AF: 0.0329 AC: 349 AN: 10592

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0649 AC: 4415 AN: 67992

Other (OTH) AF: 0.0739 AC: 156 AN: 2110

Alfa AF: 0.0536 Hom.: 99

Bravo AF: 0.0588

Asia WGS AF: 0.0150 AC: 51 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	16
DANN	Benign	0.55
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs75578132; hg19: chr2-69149986;