chr5-93583271-GTCTC-G

Variant names:

• chr5-93583271-GTCTC-G
• rs140194624
• NM_005654.6:c.-1731_-1728delCTCT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The NM_005654.6(NR2F1):​c.-1731_-1728delCTCT variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.00452 in 145,028 control chromosomes in the GnomAD database, including 4 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0045 (4 hom., cov: 25)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: NR2F1 NM_005654.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.74
• Publications: 0 publications found

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

ACMG classification

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

• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.00452 (655/145028) while in subpopulation AMR AF = 0.00939 (137/14586). AF 95% confidence interval is 0.00811. There are 4 homozygotes in GnomAd4. There are 336 alleles in the male GnomAd4 subpopulation. Median coverage is 25. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 4 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR2F1	NM_005654.6	c.-1731_-1728delCTCT		5_prime_UTR_variant	Exon 1 of 3	ENST00000327111.8	NP_005645.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR2F1	ENST00000327111.8	c.-1731_-1728delCTCT		5_prime_UTR_variant	Exon 1 of 3	1	NM_005654.6	ENSP00000325819.3

Frequencies

GnomAD3 genomes AF: 0.00451 AC: 654 AN: 144958 Hom.: 4 Cov.: 25

Gnomad AFR AF: 0.00438

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00940

Gnomad ASJ AF: 0.00443

Gnomad EAS AF: 0.00512

Gnomad SAS AF: 0.00157

Gnomad FIN AF: 0.000540

Gnomad MID AF: 0.00680

Gnomad NFE AF: 0.00433

Gnomad OTH AF: 0.00255

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 26 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 20

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 20

Other (OTH) AF: 0.00 AC: 0 AN: 4

GnomAD4 genome AF: 0.00452 AC: 655 AN: 145028 Hom.: 4 Cov.: 25 AF XY: 0.00478 AC XY: 336 AN XY: 70308

African (AFR) AF: 0.00437 AC: 172 AN: 39344

American (AMR) AF: 0.00939 AC: 137 AN: 14586

Ashkenazi Jewish (ASJ) AF: 0.00443 AC: 15 AN: 3386

East Asian (EAS) AF: 0.00513 AC: 25 AN: 4870

South Asian (SAS) AF: 0.00180 AC: 8 AN: 4450

European-Finnish (FIN) AF: 0.000540 AC: 5 AN: 9252

Middle Eastern (MID) AF: 0.00746 AC: 2 AN: 268

European-Non Finnish (NFE) AF: 0.00433 AC: 286 AN: 65998

Other (OTH) AF: 0.00252 AC: 5 AN: 1982

Alfa AF: 0.000946 Hom.: 43

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.7

Splicing

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

Other links and lift over

dbSNP: rs140194624; hg19: chr5-92918977;