rs4783187

Variant names:

• chr16-85382232-T-C
• rs4783187
• ENST00000637419.1:c.2464+24589T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637419.1(GSE1):​c.2464+24589T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.833 in 152,218 control chromosomes in the GnomAD database, including 53,014 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 0.83 (53014 hom., cov: 33)
• Consequence: GSE1 ENST00000637419.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.660
• Publications: 8 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSE1	XM_005255859.6	c.2131+24589T>C		intron_variant	Intron 2 of 16		XP_005255916.3
GSE1	XM_005255860.4	c.2131+24589T>C		intron_variant	Intron 2 of 15		XP_005255917.3
GSE1	XM_005255861.6	c.2131+24589T>C		intron_variant	Intron 2 of 15		XP_005255918.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSE1	ENST00000637419.1	c.2464+24589T>C		intron_variant	Intron 2 of 2	5		ENSP00000490157.1

Frequencies

GnomAD3 genomes AF: 0.833 AC: 126729 AN: 152100 Hom.: 52969 Cov.: 33

Gnomad AFR AF: 0.781

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.892

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.796

Gnomad FIN AF: 0.843

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.875

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.833 AC: 126827 AN: 152218 Hom.: 53014 Cov.: 33 AF XY: 0.830 AC XY: 61746 AN XY: 74432

African (AFR) AF: 0.781 AC: 32447 AN: 41538

American (AMR) AF: 0.782 AC: 11973 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.892 AC: 3097 AN: 3472

East Asian (EAS) AF: 0.825 AC: 4246 AN: 5148

South Asian (SAS) AF: 0.795 AC: 3842 AN: 4830

European-Finnish (FIN) AF: 0.843 AC: 8943 AN: 10610

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.875 AC: 59479 AN: 68008

Other (OTH) AF: 0.856 AC: 1802 AN: 2106

Alfa AF: 0.860 Hom.: 236338

Bravo AF: 0.826

Asia WGS AF: 0.789 AC: 2747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.9
DANN	Benign	0.54
PhyloP100		0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4783187; hg19: chr16-85415838;