Genetic Variant NR2F1:c.-1729_-1728dupCT (chr5-93583271-G-GTC) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_005654.6(NR2F1):c.-1729_-1728dupCT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 144,874 control chromosomes in the GnomAD database, including 1,964 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.15 ( 1964 hom., cov: 25)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

NR2F1
NM_005654.6 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.887

Publications

0 publications found

Variant links:

Genes affected

NR2F1 (HGNC:7975): (nuclear receptor subfamily 2 group F member 1) The protein encoded by this gene is a nuclear hormone receptor and transcriptional regulator. The encoded protein acts as a homodimer and binds to 5'-AGGTCA-3' repeats. Defects in this gene are a cause of Bosch-Boonstra optic atrophy syndrome (BBOAS). [provided by RefSeq, Apr 2014]

NR2F1 links:

NR2F1-AS1 (HGNC:48622): (NR2F1 antisense RNA 1)

NR2F1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR2F1	NM_005654.6 link	c.-1729_-1728dupCT		5_prime_UTR_variant	Exon 1 of 3	ENST00000327111.8	NP_005645.1	P10589

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR2F1	ENST00000327111.8 link	c.-1729_-1728dupCT		5_prime_UTR_variant	Exon 1 of 3	1	NM_005654.6	ENSP00000325819.3		P10589

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

21938

AN:

144802

Hom.:

1961

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0663

Gnomad AMI

AF:

0.231

Gnomad AMR

AF:

0.245

Gnomad ASJ

AF:

0.183

Gnomad EAS

AF:

0.194

Gnomad SAS

AF:

0.160

Gnomad FIN

AF:

0.124

Gnomad MID

AF:

0.204

Gnomad NFE

AF:

0.178

Gnomad OTH

AF:

0.163

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

GnomAD4 genome

AF:

0.151

AC:

21942

AN:

144874

Hom.:

1964

Cov.:

AF XY:

0.150

AC XY:

10499

AN XY:

70200

show subpopulations

African (AFR)

AF:

0.0662

AC:

2602

AN:

39328

American (AMR)

AF:

0.246

AC:

3585

AN:

14558

Ashkenazi Jewish (ASJ)

AF:

0.183

AC:

618

AN:

3386

East Asian (EAS)

AF:

0.194

AC:

941

AN:

4854

South Asian (SAS)

AF:

0.158

AC:

702

AN:

4450

European-Finnish (FIN)

AF:

0.124

AC:

1148

AN:

9236

Middle Eastern (MID)

AF:

0.209

AC:

AN:

268

European-Non Finnish (NFE)

AF:

0.178

AC:

11757

AN:

65926

Other (OTH)

AF:

0.165

AC:

327

AN:

1978

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

792

1584

2377

3169

3961

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.0388

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.89

Splicing

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

Publications

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chr5-93583271-G-GTC

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over