Genetic Variant GSE1:c.*419G>A (chr16-85672958-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014615.5(GSE1):c.*419G>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 0.203 in 153,256 control chromosomes in the GnomAD database, including 3,728 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 0.20 ( 3687 hom., cov: 32)

Exomes 𝑓: 0.30 ( 41 hom. )

Consequence

GSE1
NM_014615.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00600

Publications

17 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSE1	NM_014615.5 link	c.*419G>A		3_prime_UTR_variant	Exon 16 of 16	ENST00000253458.12	NP_055430.1	Q14687-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSE1	ENST00000253458.12 link	c.*419G>A		3_prime_UTR_variant	Exon 16 of 16	5	NM_014615.5	ENSP00000253458.6		Q14687-1

Frequencies

GnomAD3 genomes

AF:

0.203

AC:

30853

AN:

152010

Hom.:

3692

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0695

Gnomad AMI

AF:

0.236

Gnomad AMR

AF:

0.208

Gnomad ASJ

AF:

0.323

Gnomad EAS

AF:

0.195

Gnomad SAS

AF:

0.144

Gnomad FIN

AF:

0.229

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.276

Gnomad OTH

AF:

0.245

GnomAD4 exome

AF:

0.295

AC:

333

AN:

1128

Hom.:

Cov.:

AF XY:

0.316

AC XY:

187

AN XY:

592

show subpopulations

African (AFR)

AF:

0.0667

AC:

AN:

American (AMR)

AF:

0.280

AC:

AN:

100

Ashkenazi Jewish (ASJ)

AF:

0.265

AC:

AN:

East Asian (EAS)

AF:

0.324

AC:

AN:

South Asian (SAS)

AF:

0.0938

AC:

AN:

European-Finnish (FIN)

AF:

0.250

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.312

AC:

259

AN:

830

Other (OTH)

AF:

0.321

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.203

AC:

30843

AN:

152128

Hom.:

3687

Cov.:

AF XY:

0.199

AC XY:

14822

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.0693

AC:

2877

AN:

41518

American (AMR)

AF:

0.207

AC:

3170

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.323

AC:

1120

AN:

3472

East Asian (EAS)

AF:

0.195

AC:

1009

AN:

5174

South Asian (SAS)

AF:

0.144

AC:

696

AN:

4818

European-Finnish (FIN)

AF:

0.229

AC:

2411

AN:

10548

Middle Eastern (MID)

AF:

0.286

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.276

AC:

18744

AN:

68004

Other (OTH)

AF:

0.245

AC:

517

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1229

2458

3686

4915

6144

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

334

668

1002

1336

1670

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.248

Hom.:

15219

Bravo

AF:

0.197

Asia WGS

AF:

0.165

AC:

575

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.7

(source)

DANN

Benign

0.58

PhyloP100

0.0060

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=99/1

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over