rs8056420

Variant names:

• chr16-85378035-G-A
• rs8056420
• ENST00000637419.1:c.2464+20392G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-85378035-G-A
• chr16-85378035-G-C

Variant summary

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

The ENST00000637419.1(GSE1):​c.2464+20392G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 152,180 control chromosomes in the GnomAD database, including 43,856 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 0.75 (43856 hom., cov: 33)
• Consequence: GSE1 ENST00000637419.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSE1	XM_005255859.6	c.2131+20392G>A		intron_variant	Intron 2 of 16		XP_005255916.3
GSE1	XM_005255860.4	c.2131+20392G>A		intron_variant	Intron 2 of 15		XP_005255917.3
GSE1	XM_005255861.6	c.2131+20392G>A		intron_variant	Intron 2 of 15		XP_005255918.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSE1	ENST00000637419.1	c.2464+20392G>A		intron_variant	Intron 2 of 2	5		ENSP00000490157.1

Frequencies

GnomAD3 genomes AF: 0.746 AC: 113490 AN: 152062 Hom.: 43851 Cov.: 33

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.791

Gnomad AMR AF: 0.853

Gnomad ASJ AF: 0.861

Gnomad EAS AF: 0.863

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.746 AC: 113538 AN: 152180 Hom.: 43856 Cov.: 33 AF XY: 0.749 AC XY: 55705 AN XY: 74408

Gnomad4 AFR AF: 0.524

Gnomad4 AMR AF: 0.853

Gnomad4 ASJ AF: 0.861

Gnomad4 EAS AF: 0.863

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.829

Gnomad4 OTH AF: 0.781

Alfa AF: 0.823 Hom.: 67603

Bravo AF: 0.743

Asia WGS AF: 0.853 AC: 2961 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.7
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8056420; hg19: chr16-85411641;