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rs4986938

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001437.3(ESR2):c.*39G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 1,594,296 control chromosomes in the GnomAD database, including 102,226 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.32 ( 8374 hom., cov: 31)
Exomes 𝑓: 0.35 ( 93852 hom. )

Consequence

ESR2
NM_001437.3 3_prime_UTR

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.222
Variant links:
Genes affected
ESR2 (HGNC:3468): (estrogen receptor 2) This gene encodes a member of the family of estrogen receptors and superfamily of nuclear receptor transcription factors. The gene product contains an N-terminal DNA binding domain and C-terminal ligand binding domain and is localized to the nucleus, cytoplasm, and mitochondria. Upon binding to 17beta-estradiol or related ligands, the encoded protein forms homo- or hetero-dimers that interact with specific DNA sequences to activate transcription. Some isoforms dominantly inhibit the activity of other estrogen receptor family members. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been fully characterized. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 14-64233098-C-T is Benign according to our data. Variant chr14-64233098-C-T is described in ClinVar as [Benign]. Clinvar id is 1266011.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ESR2NM_001437.3 linkuse as main transcriptc.*39G>A 3_prime_UTR_variant 9/9 ENST00000341099.6
LOC124903328XR_007064205.1 linkuse as main transcriptn.90-1764C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ESR2ENST00000341099.6 linkuse as main transcriptc.*39G>A 3_prime_UTR_variant 9/91 NM_001437.3 P1Q92731-1

Frequencies

GnomAD3 genomes
AF:
0.323
AC:
49115
AN:
151878
Hom.:
8380
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.263
Gnomad AMI
AF:
0.615
Gnomad AMR
AF:
0.267
Gnomad ASJ
AF:
0.427
Gnomad EAS
AF:
0.124
Gnomad SAS
AF:
0.291
Gnomad FIN
AF:
0.360
Gnomad MID
AF:
0.421
Gnomad NFE
AF:
0.375
Gnomad OTH
AF:
0.332
GnomAD3 exomes
AF:
0.310
AC:
75935
AN:
244898
Hom.:
13063
AF XY:
0.318
AC XY:
41985
AN XY:
132172
show subpopulations
Gnomad AFR exome
AF:
0.257
Gnomad AMR exome
AF:
0.176
Gnomad ASJ exome
AF:
0.422
Gnomad EAS exome
AF:
0.109
Gnomad SAS exome
AF:
0.289
Gnomad FIN exome
AF:
0.361
Gnomad NFE exome
AF:
0.377
Gnomad OTH exome
AF:
0.342
GnomAD4 exome
AF:
0.355
AC:
511822
AN:
1442300
Hom.:
93852
Cov.:
34
AF XY:
0.354
AC XY:
252570
AN XY:
714176
show subpopulations
Gnomad4 AFR exome
AF:
0.260
Gnomad4 AMR exome
AF:
0.186
Gnomad4 ASJ exome
AF:
0.420
Gnomad4 EAS exome
AF:
0.134
Gnomad4 SAS exome
AF:
0.294
Gnomad4 FIN exome
AF:
0.356
Gnomad4 NFE exome
AF:
0.375
Gnomad4 OTH exome
AF:
0.352
GnomAD4 genome
AF:
0.323
AC:
49123
AN:
151996
Hom.:
8374
Cov.:
31
AF XY:
0.320
AC XY:
23803
AN XY:
74306
show subpopulations
Gnomad4 AFR
AF:
0.262
Gnomad4 AMR
AF:
0.267
Gnomad4 ASJ
AF:
0.427
Gnomad4 EAS
AF:
0.123
Gnomad4 SAS
AF:
0.291
Gnomad4 FIN
AF:
0.360
Gnomad4 NFE
AF:
0.375
Gnomad4 OTH
AF:
0.327
Alfa
AF:
0.368
Hom.:
12393
Bravo
AF:
0.312
Asia WGS
AF:
0.232
AC:
809
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJul 09, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
Cadd
Benign
5.2
Dann
Benign
0.73

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4986938; hg19: chr14-64699816; COSMIC: COSV50828487; COSMIC: COSV50828487; API