rs12918736

Variant names:

• chr16-85635384-C-G
• rs12918736
• NM_014615.5:c.226+1252C>G

Variant summary

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

The NM_014615.5(GSE1):​c.226+1252C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.37 in 152,086 control chromosomes in the GnomAD database, including 11,172 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 0.37 (11172 hom., cov: 33)
• Consequence: GSE1 NM_014615.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.88
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014615.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSE1	NM_014615.5	MANE Select	c.226+1252C>G		intron	N/A	NP_055430.1
	GSE1	NM_001278184.3		c.8-13168C>G		intron	N/A	NP_001265113.1
	GSE1	NM_001134473.3		c.-86-13168C>G		intron	N/A	NP_001127945.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSE1	ENST00000253458.12	TSL:5 MANE Select	c.226+1252C>G		intron	N/A	ENSP00000253458.6
	GSE1	ENST00000393243.5	TSL:1	c.8-13168C>G		intron	N/A	ENSP00000376934.1
	GSE1	ENST00000405402.6	TSL:1	c.-86-13168C>G		intron	N/A	ENSP00000384839.2

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56250 AN: 151968 Hom.: 11155 Cov.: 33

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.0596

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.358

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

GnomAD4 genome AF: 0.370 AC: 56302 AN: 152086 Hom.: 11172 Cov.: 33 AF XY: 0.362 AC XY: 26942 AN XY: 74336

African (AFR) AF: 0.485 AC: 20109 AN: 41484

American (AMR) AF: 0.263 AC: 4023 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1292 AN: 3470

East Asian (EAS) AF: 0.0598 AC: 309 AN: 5170

South Asian (SAS) AF: 0.283 AC: 1362 AN: 4820

European-Finnish (FIN) AF: 0.357 AC: 3780 AN: 10588

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24211 AN: 67940

Other (OTH) AF: 0.357 AC: 755 AN: 2114

Alfa AF: 0.358 Hom.: 1251

Bravo AF: 0.367

Asia WGS AF: 0.191 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.54
PhyloP100		-1.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12918736; hg19: chr16-85668990;