chr14-76485030-G-T

Position:

• chr14-76485030-G-T

Variant summary

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

The NM_001379180.1(ESRRB):​c.850+2271G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,070 control chromosomes in the GnomAD database, including 1,048 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 0.11 (1048 hom., cov: 32)
• Consequence: ESRRB NM_001379180.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.523

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]

ESRRB (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ESRRB	NM_001379180.1	c.850+2271G>T		intron_variant		ENST00000644823.1	NP_001366109.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ESRRB	ENST00000644823.1	c.850+2271G>T		intron_variant			NM_001379180.1	ENSP00000493776.1

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17368 AN: 151952 Hom.: 1049 Cov.: 32

Gnomad AFR AF: 0.0809

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.114 AC: 17357 AN: 152070 Hom.: 1048 Cov.: 32 AF XY: 0.115 AC XY: 8570 AN XY: 74340

Gnomad4 AFR AF: 0.0807

Gnomad4 AMR AF: 0.141

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.117

Alfa AF: 0.121 Hom.: 2405

Bravo AF: 0.113

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	3.6
DANN	Benign	0.67

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: rs7155416; hg19: chr14-76951373;