15-96340092-G-C

Variant names:

• chr15-96340092-G-C
• rs11045
• NM_021005.4:c.*2470G>C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_021005.4(NR2F2):​c.*2470G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: NR2F2 NM_021005.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.619

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]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NR2F2	NM_021005.4	c.*2470G>C		3_prime_UTR_variant	Exon 3 of 3	ENST00000394166.8	NP_066285.1
NR2F2	NM_001145155.2	c.*2470G>C		3_prime_UTR_variant	Exon 3 of 3		NP_001138627.1
NR2F2	NM_001145156.1	c.*2470G>C		3_prime_UTR_variant	Exon 3 of 3		NP_001138628.1
NR2F2	NM_001145157.2	c.*2470G>C		3_prime_UTR_variant	Exon 3 of 3		NP_001138629.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NR2F2	ENST00000394166.8	c.*2470G>C		3_prime_UTR_variant	Exon 3 of 3	1	NM_021005.4	ENSP00000377721.3
NR2F2	ENST00000394171.6	c.*2470G>C		3_prime_UTR_variant	Exon 3 of 3	2		ENSP00000377726.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	14
DANN	Benign	0.72

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

Publications

LitVar

Other links and lift over

dbSNP: rs11045; hg19: chr15-96883321;