Variant 16-85634077-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2

The NM_014615.5(GSE1):c.171C>T(p.Ser57=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00803 in 1,603,042 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0068 ( 9 hom., cov: 33)

Exomes 𝑓: 0.0082 ( 68 hom. )

Consequence

GSE1
NM_014615.5 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.29

Variant links:

Genes affected

GSE1 (HGNC:28979): (Gse1 coiled-coil protein) This gene encodes a proline-rich protein with coiled coil domains that may be a subunit of a BRAF35-HDAC (BHC) histone deacetylase complex. This gene may function as an oncogene in breast cancer and enhanced expression of the encoded protein has been observed in breast cancer patients. [provided by RefSeq, May 2017]

GSE1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.4).

BP6

Variant 16-85634077-C-T is Benign according to our data. Variant chr16-85634077-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2646933.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=1.29 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 9 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GSE1	NM_014615.5 linkuse as main transcript	c.171C>T	p.Ser57=	synonymous_variant	2/16	ENST00000253458.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GSE1	ENST00000253458.12 linkuse as main transcript	c.171C>T	p.Ser57=	synonymous_variant	2/16	5	NM_014615.5	A2	Q14687-1

Frequencies

GnomAD3 genomes

AF:

0.00677

AC:

1030

AN:

152230

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00164

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.00916

Gnomad ASJ

AF:

0.0441

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00434

Gnomad FIN

AF:

0.000847

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00908

Gnomad OTH

AF:

0.00861

GnomAD3 exomes

AF:

0.00721

AC:

1633

AN:

226504

Hom.:

AF XY:

0.00688

AC XY:

858

AN XY:

124726

show subpopulations

Gnomad AFR exome

AF:

0.00104

Gnomad AMR exome

AF:

0.00674

Gnomad ASJ exome

AF:

0.0375

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00317

Gnomad FIN exome

AF:

0.00113

Gnomad NFE exome

AF:

0.00891

Gnomad OTH exome

AF:

0.00867

GnomAD4 exome

AF:

0.00817

AC:

11846

AN:

1450698

Hom.:

Cov.:

AF XY:

0.00818

AC XY:

5902

AN XY:

721178

show subpopulations

Gnomad4 AFR exome

AF:

0.00169

Gnomad4 AMR exome

AF:

0.00668

Gnomad4 ASJ exome

AF:

0.0371

Gnomad4 EAS exome

AF:

0.0000254

Gnomad4 SAS exome

AF:

0.00306

Gnomad4 FIN exome

AF:

0.00103

Gnomad4 NFE exome

AF:

0.00870

Gnomad4 OTH exome

AF:

0.00939

GnomAD4 genome

AF:

0.00675

AC:

1029

AN:

152344

Hom.:

Cov.:

AF XY:

0.00651

AC XY:

485

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.00164

Gnomad4 AMR

AF:

0.00915

Gnomad4 ASJ

AF:

0.0441

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00414

Gnomad4 FIN

AF:

0.000847

Gnomad4 NFE

AF:

0.00909

Gnomad4 OTH

AF:

0.00852

Alfa

AF:

0.0111

Hom.:

Bravo

AF:

0.00713

Asia WGS

AF:

0.00289

AC:

AN:

3472

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

GSE1: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.40

CADD

Benign

8.2

DANN

Benign

0.97

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over