16-85672958-G-A

Position:

• chr16-85672958-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
GSE1	NM_014615.5	c.*419G>A		3_prime_UTR_variant	16/16	ENST00000253458.12	NP_055430.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GSE1	ENST00000253458.12	c.*419G>A		3_prime_UTR_variant	16/16	5	NM_014615.5	ENSP00000253458	A2

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30853 AN: 152010 Hom.: 3692 Cov.: 32

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.: 41 Cov.: 0 AF XY: 0.316 AC XY: 187 AN XY: 592

Gnomad4 AFR exome AF: 0.0667

Gnomad4 AMR exome AF: 0.280

Gnomad4 ASJ exome AF: 0.265

Gnomad4 EAS exome AF: 0.324

Gnomad4 SAS exome AF: 0.0938

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.312

Gnomad4 OTH exome AF: 0.321

GnomAD4 genome AF: 0.203 AC: 30843 AN: 152128 Hom.: 3687 Cov.: 32 AF XY: 0.199 AC XY: 14822 AN XY: 74336

Gnomad4 AFR AF: 0.0693

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.229

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.245

Alfa AF: 0.264 Hom.: 9473

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
DANN	Benign	0.58
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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

LitVar

Other links and lift over

dbSNP: rs709805; hg19: chr16-85706564;