NM_001438.4:c.862+21024T>C

Variant names:

• chr1-216543195-A-G
• rs12757165
• NM_001438.4:c.862+21024T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001438.4(ESRRG):​c.862+21024T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,886 control chromosomes in the GnomAD database, including 7,460 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 0.29 (7460 hom., cov: 33)
• Consequence: ESRRG NM_001438.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350
• Publications: 19 publications found

Genes affected

ESRRG (HGNC:3474): (estrogen related receptor gamma) This gene encodes a member of the estrogen receptor-related receptor (ESRR) family, which belongs to the nuclear hormone receptor superfamily. All members of the ESRR family share an almost identical DNA binding domain, which is composed of two C4-type zinc finger motifs. The ESRR members are orphan nuclear receptors; they bind to the estrogen response element and steroidogenic factor 1 response element, and activate genes controlled by both response elements in the absence of any ligands. The ESRR family is closely related to the estrogen receptor (ER) family. They share target genes, co-regulators and promoters, and by targeting the same set of genes, the ESRRs seem to interfere with the ER-mediated estrogen response in various ways. It has been reported that the family member encoded by this gene functions as a transcriptional activator of DNA cytosine-5-methyltransferases 1 (Dnmt1) expression by direct binding to its response elements in the DNMT1 promoters, modulates cell proliferation and estrogen signaling in breast cancer, and negatively regulates bone morphogenetic protein 2-induced osteoblast differentiation and bone formation. Multiple alternatively spliced transcript variants have been identified, which mainly differ at the 5' end and some of which encode protein isoforms differing in the N-terminal region. [provided by RefSeq, Aug 2011]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001438.4. 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
	ESRRG	NM_001438.4	MANE Select	c.862+21024T>C		intron	N/A	NP_001429.2
	ESRRG	NM_001243518.2		c.898+21024T>C		intron	N/A	NP_001230447.1
	ESRRG	NM_001134285.3		c.793+21024T>C		intron	N/A	NP_001127757.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ESRRG	ENST00000408911.8	TSL:1 MANE Select	c.862+21024T>C		intron	N/A	ENSP00000386171.3
	ESRRG	ENST00000366937.5	TSL:1	c.898+21024T>C		intron	N/A	ENSP00000355904.1
	ESRRG	ENST00000359162.6	TSL:1	c.793+21024T>C		intron	N/A	ENSP00000352077.2

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44284 AN: 151768 Hom.: 7448 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.277

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.298

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.292 AC: 44306 AN: 151886 Hom.: 7460 Cov.: 33 AF XY: 0.298 AC XY: 22088 AN XY: 74226

African (AFR) AF: 0.125 AC: 5189 AN: 41478

American (AMR) AF: 0.397 AC: 6038 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.277 AC: 962 AN: 3468

East Asian (EAS) AF: 0.334 AC: 1709 AN: 5120

South Asian (SAS) AF: 0.285 AC: 1372 AN: 4812

European-Finnish (FIN) AF: 0.395 AC: 4183 AN: 10586

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23745 AN: 67890

Other (OTH) AF: 0.299 AC: 630 AN: 2108

Alfa AF: 0.326 Hom.: 15868

Bravo AF: 0.288

Asia WGS AF: 0.317 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.59
PhyloP100		0.035
Mutation Taster		=100/0	polymorphism (auto)

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: rs12757165; hg19: chr1-216716537;