rs9383939

chr6-151685043-G-Achr6-151685043-G-C

Variant summary

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

The ENST00000473497.5(ESR1):n.74-16832G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.095 in 150,772 control chromosomes in the GnomAD database, including 926 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 0.095 (926 hom., cov: 31)
• Consequence: ESR1 ENST00000473497.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ESR1	NM_001385568.1	c.-201-16832G>A		intron_variant
ESR1	XM_017010377.2	c.-201-16832G>A		intron_variant
ESR1	XM_017010380.2	c.-71+28280G>A		intron_variant
ESR1	XM_047418290.1	c.-201-16832G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ESR1	ENST00000473497.5	n.74-16832G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.0951 AC: 14326 AN: 150708 Hom.: 926 Cov.: 31

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.0737

Gnomad ASJ AF: 0.0616

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.0937

Gnomad FIN AF: 0.0256

Gnomad MID AF: 0.0682

Gnomad NFE AF: 0.0680

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0950 AC: 14330 AN: 150772 Hom.: 926 Cov.: 31 AF XY: 0.0939 AC XY: 6905 AN XY: 73568

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.0737

Gnomad4 ASJ AF: 0.0616

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.0934

Gnomad4 FIN AF: 0.0256

Gnomad4 NFE AF: 0.0680

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0685 Hom.: 544

Bravo AF: 0.101

Asia WGS AF: 0.217 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.1
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9383939; hg19: chr6-152006178;