dbSNP rs10187256: GKN3P:n.176A>G (chr2-68922849-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.60

Publications

2 publications found

Variant links:

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]

GKN3P links:

ENSG00000307469 (HGNC:):

ENSG00000307469 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GKN3P		n.68922849A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GKN3P	ENST00000637675.1 link	n.176A>G		non_coding_transcript_exon_variant	Exon 3 of 6	5
ENSG00000307469	ENST00000826466.1 link	n.96+8562T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

28863

AN:

152074

Hom.:

5716

Cov.:

show subpopulations

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.:

AF XY:

0.0769

AC XY:

9594

AN XY:

124800

show subpopulations

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:

AN:

22894

South Asian (SAS)

AF:

0.0290

AC:

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

892

1784

2675

3567

4459

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

152

228

304

380

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.190

AC:

28935

AN:

152192

Hom.:

5743

Cov.:

AF XY:

0.184

AC XY:

13694

AN XY:

74426

show subpopulations

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:

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0680

AC:

4625

AN:

68020

Other (OTH)

AF:

0.171

AC:

361

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

898

1796

2695

3593

4491

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

244

488

732

976

1220

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

(source)

DANN

Benign

0.44

PhyloP100

2.6

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over