dbSNP rs134882: OGFRP1:n.1348T>C (chr22-42274959-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000332965.4(OGFRP1):n.1348T>C 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 0.353 in 152,200 control chromosomes in the GnomAD database, including 11,207 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 0.35 ( 11196 hom., cov: 32)

Exomes 𝑓: 0.48 ( 11 hom. )

Consequence

OGFRP1
ENST00000332965.4 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

14 publications found

Variant links:

Genes affected

OGFRP1 (HGNC:50511): (opioid growth factor receptor pseudogene 1)

OGFRP1 links:

TCF20 (HGNC:11631): (transcription factor 20) This gene encodes a transcription factor that recognizes the platelet-derived growth factor-responsive element in the matrix metalloproteinase 3 promoter. The encoded protein is thought to be a transcriptional coactivator, enhancing the activity of transcription factors such as JUN and SP1. Mutations in this gene are associated with autism spectrum disorders. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2015]

TCF20 Gene-Disease associations (from GenCC):

developmental delay with variable intellectual impairment and behavioral abnormalities
Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: ClinGen, Labcorp Genetics (formerly Invitae), G2P, Illumina
syndromic intellectual disability
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

TCF20 links:

Genome browser will be placed here

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=-0.89).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000332965.4. 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
	TCF20	NM_005650.4		c.-37+8868A>G		intron	N/A	NP_005641.1
	OGFRP1	NR_036498.1		n.*97T>C		downstream_gene	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
OGFRP1	ENST00000332965.4	TSL:1	n.1348T>C	non_coding_transcript_exon	Exon 2 of 2
TCF20	ENST00000359486.8	TSL:1	c.-37+8868A>G	intron	N/A	ENSP00000352463.3
TCF20	ENST00000675876.1		c.-37+43105A>G	intron	N/A	ENSP00000502259.1

Frequencies

GnomAD3 genomes

AF:

0.353

AC:

53672

AN:

151998

Hom.:

11181

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.330

Gnomad AMR

AF:

0.439

Gnomad ASJ

AF:

0.369

Gnomad EAS

AF:

0.324

Gnomad SAS

AF:

0.471

Gnomad FIN

AF:

0.449

Gnomad MID

AF:

0.408

Gnomad NFE

AF:

0.452

Gnomad OTH

AF:

0.377

GnomAD4 exome

AF:

0.476

AC:

AN:

Hom.:

Cov.:

AF XY:

0.471

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.456

AC:

AN:

Other (OTH)

AF:

0.667

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.528

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.353

AC:

53687

AN:

152116

Hom.:

11196

Cov.:

AF XY:

0.357

AC XY:

26530

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.121

AC:

5038

AN:

41522

American (AMR)

AF:

0.439

AC:

6706

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.369

AC:

1280

AN:

3470

East Asian (EAS)

AF:

0.324

AC:

1677

AN:

5176

South Asian (SAS)

AF:

0.472

AC:

2273

AN:

4818

European-Finnish (FIN)

AF:

0.449

AC:

4742

AN:

10568

Middle Eastern (MID)

AF:

0.401

AC:

118

AN:

294

European-Non Finnish (NFE)

AF:

0.452

AC:

30741

AN:

67958

Other (OTH)

AF:

0.384

AC:

811

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1645

3290

4936

6581

8226

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

520

1040

1560

2080

2600

<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:

0.406

Hom.:

20185

Bravo

AF:

0.342

Asia WGS

AF:

0.414

AC:

1438

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.28

(source)

DANN

Benign

0.74

PhyloP100

-1.1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over