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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637419.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSE1	ENST00000637419.1	TSL:5	c.2464+24589T>C		intron	N/A	ENSP00000490157.1	A0A1B0GUL3

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4783187;

hg19: chr16-85415838;