rs2360997

Positions:

• chr14-76346148-G-C

Variant summary

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

The NM_001411038.1(ESRRB):​c.2+35232G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.809 in 152,118 control chromosomes in the GnomAD database, including 50,277 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 0.81 (50277 hom., cov: 32)
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ESRRB	NM_001411038.1	c.2+35232G>C		intron_variant
ESRRB	XM_047431079.1	c.-68+35232G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ESRRB	ENST00000512784.6	c.2+35232G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.809 AC: 123023 AN: 152000 Hom.: 50237 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.874

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.960

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.834

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.809 AC: 123122 AN: 152118 Hom.: 50277 Cov.: 32 AF XY: 0.813 AC XY: 60438 AN XY: 74368

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.890

Gnomad4 ASJ AF: 0.874

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.960

Gnomad4 FIN AF: 0.745

Gnomad4 NFE AF: 0.834

Gnomad4 OTH AF: 0.835

Alfa AF: 0.839 Hom.: 29802

Bravo AF: 0.815

Asia WGS AF: 0.956 AC: 3320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.6
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2360997; hg19: chr14-76812491;