rs2361000

chr14-76355290-T-Cchr14-76355290-T-G

Variant summary

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

The NM_001411038.1(ESRRB):c.2+44374T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,110 control chromosomes in the GnomAD database, including 3,647 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 0.20 (3647 hom., cov: 31)
• Consequence: ESRRB NM_001411038.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

Genes affected

ESRRB (HGNC:3473): (estrogen related receptor beta) This gene encodes a protein with similarity to the estrogen receptor. Its function is unknown; however, a similar protein in mouse plays an essential role in placental development. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ESRRB	NM_001411038.1	c.2+44374T>C		intron_variant
ESRRB	XM_047431079.1	c.-68+44374T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ESRRB	ENST00000512784.6	c.2+44374T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29804 AN: 151992 Hom.: 3651 Cov.: 31

Gnomad AFR AF: 0.0565

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.242

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.196 AC: 29799 AN: 152110 Hom.: 3647 Cov.: 31 AF XY: 0.196 AC XY: 14541 AN XY: 74364

Gnomad4 AFR AF: 0.0564

Gnomad4 AMR AF: 0.242

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.191

Alfa AF: 0.181 Hom.: 681

Bravo AF: 0.186

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.073
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2361000; hg19: chr14-76821633;