rs1899165403

Variant names:

• chr15-96332153-C-G
• rs1899165403
• NM_021005.4:c.48C>G

Your query was ambiguous. Multiple possible variants found:

• chr15-96332153-C-G
• chr15-96332153-C-T

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_021005.4(NR2F2):​c.48C>G​(p.Pro16Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000333 in 1,203,006 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P16P) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 0.0000033 (0 hom.)
• Consequence: NR2F2 NM_021005.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.978
• Publications: 0 publications found

Genes affected

NR2F2 (HGNC:7976): (nuclear receptor subfamily 2 group F member 2) This gene encodes a member of the steroid thyroid hormone superfamily of nuclear receptors. The encoded protein is a ligand inducible transcription factor that is involved in the regulation of many different genes. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]

NR2F2-AS1 (HGNC:44222): (NR2F2 antisense RNA 1)

ACMG classification

Our verdict: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BP7: Synonymous conserved (PhyloP=0.978 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021005.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR2F2	NM_021005.4	MANE Select	c.48C>G	p.Pro16Pro	synonymous	Exon 1 of 3	NP_066285.1	F1D8R0
	NR2F2	NM_001145155.2		c.44-1923C>G		intron	N/A	NP_001138627.1	P24468-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR2F2	ENST00000394166.8	TSL:1 MANE Select	c.48C>G	p.Pro16Pro	synonymous	Exon 1 of 3	ENSP00000377721.3	P24468-1
	NR2F2	ENST00000421109.6	TSL:1	c.44-1923C>G		intron	N/A	ENSP00000401674.2	P24468-2
	NR2F2	ENST00000961130.1		c.48C>G	p.Pro16Pro	synonymous	Exon 2 of 4	ENSP00000631189.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000332 AC: 4 AN: 1203006 Hom.: 0 Cov.: 30 AF XY: 0.00000340 AC XY: 2 AN XY: 587416

African (AFR) AF: 0.00 AC: 0 AN: 23888

American (AMR) AF: 0.00 AC: 0 AN: 12826

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17208

East Asian (EAS) AF: 0.00 AC: 0 AN: 26522

South Asian (SAS) AF: 0.00 AC: 0 AN: 46798

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 38110

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3438

European-Non Finnish (NFE) AF: 0.00000304 AC: 3 AN: 985868

Other (OTH) AF: 0.0000207 AC: 1 AN: 48348

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	13
DANN	Benign	0.92
PhyloP100		0.98
PromoterAI		0.0058	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1899165403; hg19: chr15-96875382;