16-85634339-C-G

Variant names:

• chr16-85634339-C-G
• rs7405052
• NM_014615.5:c.226+207C>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+207C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,186 control chromosomes in the GnomAD database, including 24,975 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 0.57 (24975 hom., cov: 35)
• Consequence: GSE1 NM_014615.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSE1	NM_014615.5	MANE Select	c.226+207C>G		intron	N/A	NP_055430.1	Q14687-1
	GSE1	NM_001278184.3		c.8-14213C>G		intron	N/A	NP_001265113.1	Q14687-3
	GSE1	NM_001134473.3		c.-86-14213C>G		intron	N/A	NP_001127945.1	Q14687-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSE1	ENST00000253458.12	TSL:5 MANE Select	c.226+207C>G		intron	N/A	ENSP00000253458.6	Q14687-1
	GSE1	ENST00000393243.5	TSL:1	c.8-14213C>G		intron	N/A	ENSP00000376934.1	Q14687-3
	GSE1	ENST00000405402.6	TSL:1	c.-86-14213C>G		intron	N/A	ENSP00000384839.2	Q14687-2

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85931 AN: 152068 Hom.: 24965 Cov.: 35

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.570

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.565 AC: 85987 AN: 152186 Hom.: 24975 Cov.: 35 AF XY: 0.562 AC XY: 41833 AN XY: 74404

African (AFR) AF: 0.445 AC: 18459 AN: 41504

American (AMR) AF: 0.570 AC: 8719 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2174 AN: 3470

East Asian (EAS) AF: 0.402 AC: 2078 AN: 5174

South Asian (SAS) AF: 0.519 AC: 2509 AN: 4832

European-Finnish (FIN) AF: 0.618 AC: 6557 AN: 10604

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43616 AN: 67988

Other (OTH) AF: 0.575 AC: 1214 AN: 2112

Alfa AF: 0.601 Hom.: 3392

Bravo AF: 0.555

Asia WGS AF: 0.475 AC: 1653 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	1.9
DANN	Benign	0.61
PhyloP100		-0.54
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs7405052; hg19: chr16-85667945;