rs11947310

chr4-15742953-A-Cchr4-15742953-A-Gchr4-15742953-A-T

Variant summary

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

The XM_011513878.4(BST1):c.851+20019A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,296 control chromosomes in the GnomAD database, including 3,289 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 (3289 hom., cov: 33)
• Consequence: BST1 XM_011513878.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

Genes affected

BST1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BST1	XM_011513878.4	c.851+20019A>C		intron_variant
BST1	XM_017008566.3	c.852-16191A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30884 AN: 152178 Hom.: 3287 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.201

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.203 AC: 30900 AN: 152296 Hom.: 3289 Cov.: 33 AF XY: 0.202 AC XY: 15021 AN XY: 74458

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.201

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.216

Alfa AF: 0.150 Hom.: 544

Bravo AF: 0.208

Asia WGS AF: 0.239 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	5.4
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11947310; hg19: chr4-15744576;