Variant rs7186021 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000637419.1(GSE1):c.2464+94810A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,090 control chromosomes in the GnomAD database, including 17,932 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 0.48 ( 17932 hom., cov: 34)

Consequence

GSE1
ENST00000637419.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.426

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:

LOC124903738 (HGNC:):

LOC124903738 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein
GSE1	XM_005255859.6 linkuse as main transcript	c.2131+94810A>C	intron_variant	XP_005255916.3
GSE1	XM_005255860.4 linkuse as main transcript	c.2131+94810A>C	intron_variant	XP_005255917.3
GSE1	XM_005255861.6 linkuse as main transcript	c.2131+94810A>C	intron_variant	XP_005255918.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSE1	ENST00000637419.1 linkuse as main transcript	c.2464+94810A>C		intron_variant		5		ENSP00000490157.1		A0A1B0GUL3

Frequencies

GnomAD3 genomes

AF:

0.483

AC:

73423

AN:

151972

Hom.:

17914

Cov.:

show subpopulations

Gnomad AFR

AF:

0.467

Gnomad AMI

AF:

0.492

Gnomad AMR

AF:

0.551

Gnomad ASJ

AF:

0.428

Gnomad EAS

AF:

0.664

Gnomad SAS

AF:

0.539

Gnomad FIN

AF:

0.419

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.473

Gnomad OTH

AF:

0.487

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

GnomAD4 genome

AF:

0.483

AC:

73478

AN:

152090

Hom.:

17932

Cov.:

AF XY:

0.485

AC XY:

36078

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.467

Gnomad4 AMR

AF:

0.551

Gnomad4 ASJ

AF:

0.428

Gnomad4 EAS

AF:

0.663

Gnomad4 SAS

AF:

0.539

Gnomad4 FIN

AF:

0.419

Gnomad4 NFE

AF:

0.473

Gnomad4 OTH

AF:

0.487

Alfa

AF:

0.469

Hom.:

24529

Bravo

AF:

0.492

Asia WGS

AF:

0.565

AC:

1964

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.4

DANN

Benign

0.70

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over