Menu
GeneBe

rs1256049

chr14-64257333-C-T

Variant summary

Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BA1

The NM_001437.3(ESR2):c.984G>A(p.Val328=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0661 in 152108 control chromosomes in the gnomAD Genomes database, including 674 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (β˜…β˜…).

Frequency

Genomes: 𝑓 0.066 ( 674 hom., cov: 31)
Exomes 𝑓: 0.067 ( 1557 hom. )

Consequence

ESR2
NM_001437.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0340

Links

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -19 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.38).
BP6
?
Variant 14-64257333-C-T is Benign according to our data. Variant chr14-64257333-C-T is described in ClinVar as [Benign]. Clinvar id is 1228925. Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.034 with no splicing effect.
BA1
?
GnomAd highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ESR2NM_001437.3 linkuse as main transcriptc.984G>A p.Val328= synonymous_variant 6/9 ENST00000341099.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ESR2ENST00000341099.6 linkuse as main transcriptc.984G>A p.Val328= synonymous_variant 6/91 NM_001437.3 P1Q92731-1

Frequencies

GnomAD3 genomes
AF:
0.0661
AC:
10050
AN:
152108
Hom.:
674
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0893
Gnomad AMI
AF:
0.00658
Gnomad AMR
AF:
0.0441
Gnomad ASJ
AF:
0.0110
Gnomad EAS
AF:
0.368
Gnomad SAS
AF:
0.0435
Gnomad FIN
AF:
0.0880
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.0364
Gnomad OTH
AF:
0.0517
GnomAD3 exomes
AF:
0.0667
AC:
16779
AN:
251436
Hom.:
1557
AF XY:
0.0624
AC XY:
8474
AN XY:
135902
show subpopulations
Gnomad AFR exome
AF:
0.0913
Gnomad AMR exome
AF:
0.0377
Gnomad ASJ exome
AF:
0.0122
Gnomad EAS exome
AF:
0.368
Gnomad SAS exome
AF:
0.0336
Gnomad FIN exome
AF:
0.0798
Gnomad NFE exome
AF:
0.0355
Gnomad OTH exome
AF:
0.0490
GnomAD4 exome
AF:
0.0445
AC:
64963
AN:
1461140
Hom.:
3351
AF XY:
0.0438
AC XY:
31842
AN XY:
726868
show subpopulations
Gnomad4 AFR exome
AF:
0.0923
Gnomad4 AMR exome
AF:
0.0388
Gnomad4 ASJ exome
AF:
0.0117
Gnomad4 EAS exome
AF:
0.320
Gnomad4 SAS exome
AF:
0.0332
Gnomad4 FIN exome
AF:
0.0781
Gnomad4 NFE exome
AF:
0.0329
Gnomad4 OTH exome
AF:
0.0567
Alfa
AF:
0.0409
Hom.:
259
Bravo
AF:
0.0651
Asia WGS
AF:
0.180
AC:
623
AN:
3478
EpiCase
AF:
0.0281
EpiControl
AF:
0.0314

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:2
Benign, criteria provided, single submitterclinical testingInvitaeOct 27, 2022- -
Benign, criteria provided, single submitterclinical testingGeneDxJul 09, 2018This variant is associated with the following publications: (PMID: 11231990) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.38
Cadd
Benign
7.9
Dann
Benign
0.63

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: rs1256049; hg19: chr14-64724051; COSMIC: COSV50829277;