4-15741950-C-T

Position:

• chr4-15741950-C-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+19016C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,096 control chromosomes in the GnomAD database, including 4,850 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 0.24 (4850 hom., cov: 32)
• Consequence: BST1 XM_011513878.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.910

Genes affected

BST1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BST1	XM_011513878.4	c.851+19016C>T		intron_variant
BST1	XM_017008566.3	c.852-17194C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36803 AN: 151978 Hom.: 4842 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.246

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

GnomAD4 genome AF: 0.242 AC: 36837 AN: 152096 Hom.: 4850 Cov.: 32 AF XY: 0.239 AC XY: 17783 AN XY: 74368

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.383

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.244

Alfa AF: 0.207 Hom.: 7569

Bravo AF: 0.252

Asia WGS AF: 0.249 AC: 869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.55
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10019008; hg19: chr4-15743573;