rs3020364

Positions:

• chr6-152045983-A-G
• chr6-152045983-A-T

Variant summary

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

The NM_000125.4(ESR1):​c.1236-15008A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 152,064 control chromosomes in the GnomAD database, including 14,959 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 0.42 (14959 hom., cov: 32)
• Consequence: ESR1 NM_000125.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

Genes affected

ESR1 (HGNC:3467): (estrogen receptor 1) This gene encodes an estrogen receptor and ligand-activated transcription factor. The canonical protein contains an N-terminal ligand-independent transactivation domain, a central DNA binding domain, a hinge domain, and a C-terminal ligand-dependent transactivation domain. The protein localizes to the nucleus where it may form either a homodimer or a heterodimer with estrogen receptor 2. The protein encoded by this gene regulates the transcription of many estrogen-inducible genes that play a role in growth, metabolism, sexual development, gestation, and other reproductive functions and is expressed in many non-reproductive tissues. The receptor encoded by this gene plays a key role in breast cancer, endometrial cancer, and osteoporosis. This gene is reported to have dozens of transcript variants due to the use of alternate promoters and alternative splicing, however, the full-length nature of many of these variants remain uncertain. [provided by RefSeq, Jul 2020]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ESR1	NM_000125.4	c.1236-15008A>G		intron_variant		ENST00000206249.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ESR1	ENST00000206249.8	c.1236-15008A>G		intron_variant		1	NM_000125.4	P1

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64073 AN: 151946 Hom.: 14942 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.422 AC: 64144 AN: 152064 Hom.: 14959 Cov.: 32 AF XY: 0.423 AC XY: 31447 AN XY: 74326

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.253

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.556

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.393

Alfa AF: 0.376 Hom.: 1866

Bravo AF: 0.413

Asia WGS AF: 0.572 AC: 1991 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.27
DANN	Benign	0.72

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: rs3020364; hg19: chr6-152367118; COSMIC: COSV52801136;