chr16-85452453-A-C

Variant names:

• chr16-85452453-A-C
• rs7186021
• XR_007065157.1:n.10216T>G

Variant summary

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

The XR_007065157.1(LOC124903738):​n.10216T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,090 control chromosomes in the GnomAD database, including 17,932 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 0.48 (17932 hom., cov: 34)
• Consequence: LOC124903738 XR_007065157.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 1 publications found

Genes affected

LOC124903738 (HGNC:):

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903738	XR_007065157.1	n.10216T>G		non_coding_transcript_exon_variant	Exon 1 of 2
GSE1	XM_005255859.6	c.2131+94810A>C		intron_variant	Intron 2 of 16		XP_005255916.3
GSE1	XM_005255860.4	c.2131+94810A>C		intron_variant	Intron 2 of 15		XP_005255917.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSE1	ENST00000637419.1	c.2464+94810A>C		intron_variant	Intron 2 of 2	5		ENSP00000490157.1

Frequencies

GnomAD3 genomes AF: 0.483 AC: 73423 AN: 151972 Hom.: 17914 Cov.: 34

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.483 AC: 73478 AN: 152090 Hom.: 17932 Cov.: 34 AF XY: 0.485 AC XY: 36078 AN XY: 74358

African (AFR) AF: 0.467 AC: 19358 AN: 41468

American (AMR) AF: 0.551 AC: 8427 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1484 AN: 3470

East Asian (EAS) AF: 0.663 AC: 3415 AN: 5150

South Asian (SAS) AF: 0.539 AC: 2597 AN: 4820

European-Finnish (FIN) AF: 0.419 AC: 4436 AN: 10590

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32140 AN: 67970

Other (OTH) AF: 0.487 AC: 1030 AN: 2116

Alfa AF: 0.474 Hom.: 44436

Bravo AF: 0.492

Asia WGS AF: 0.565 AC: 1964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.4
DANN	Benign	0.70
PhyloP100		-0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7186021; hg19: chr16-85486059;