rs3783736

chr14-64284654-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001437.3(ESR2):c.-90-1579C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 151,704 control chromosomes in the GnomAD database, including 14,445 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 0.43 (14445 hom., cov: 30)
• Consequence: ESR2 NM_001437.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

ESR2 (HGNC:3468): (estrogen receptor 2) This gene encodes a member of the family of estrogen receptors and superfamily of nuclear receptor transcription factors. The gene product contains an N-terminal DNA binding domain and C-terminal ligand binding domain and is localized to the nucleus, cytoplasm, and mitochondria. Upon binding to 17beta-estradiol or related ligands, the encoded protein forms homo- or hetero-dimers that interact with specific DNA sequences to activate transcription. Some isoforms dominantly inhibit the activity of other estrogen receptor family members. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been fully characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ESR2	NM_001437.3	c.-90-1579C>A		intron_variant		ENST00000341099.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ESR2	ENST00000341099.6	c.-90-1579C>A		intron_variant		1	NM_001437.3	P1

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65091 AN: 151586 Hom.: 14439 Cov.: 30

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.429 AC: 65127 AN: 151704 Hom.: 14445 Cov.: 30 AF XY: 0.425 AC XY: 31485 AN XY: 74134

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.384

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.429

Alfa AF: 0.425 Hom.: 18657

Bravo AF: 0.428

Asia WGS AF: 0.338 AC: 1176 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.21
Dann	Benign	0.42

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: rs3783736; hg19: chr14-64751372;