16-85481516-T-G

Variant names:

• chr16-85481516-T-G
• rs8053194
• ENST00000637419.1:c.2464+123873T>G

Variant summary

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

The ENST00000637419.1(GSE1):​c.2464+123873T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 152,008 control chromosomes in the GnomAD database, including 26,504 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 0.59 (26504 hom., cov: 32)
• Consequence: GSE1 ENST00000637419.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 2 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=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.595 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+123873T>G		intron	N/A	ENSP00000490157.1	A0A1B0GUL3

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89414 AN: 151888 Hom.: 26493 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.589 AC: 89467 AN: 152008 Hom.: 26504 Cov.: 32 AF XY: 0.593 AC XY: 44071 AN XY: 74314

African (AFR) AF: 0.565 AC: 23427 AN: 41430

American (AMR) AF: 0.582 AC: 8888 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2037 AN: 3470

East Asian (EAS) AF: 0.445 AC: 2295 AN: 5160

South Asian (SAS) AF: 0.537 AC: 2592 AN: 4824

European-Finnish (FIN) AF: 0.718 AC: 7583 AN: 10560

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.600 AC: 40771 AN: 67970

Other (OTH) AF: 0.580 AC: 1226 AN: 2112

Alfa AF: 0.581 Hom.: 11944

Bravo AF: 0.580

Asia WGS AF: 0.501 AC: 1744 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.86
DANN	Benign	0.90
PhyloP100		-0.18

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: rs8053194;

hg19: chr16-85515122;