rs7219986

Positions:

• chr17-55185846-C-T

Variant summary

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

The XM_047435714.1(STXBP4):​c.*9972C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 152,010 control chromosomes in the GnomAD database, including 1,050 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 0.081 (1050 hom., cov: 31)
• Consequence: STXBP4 XM_047435714.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607

Genes affected

STXBP4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STXBP4	XM_047435714.1	c.*9972C>T		3_prime_UTR_variant	18/18
STXBP4	XR_007065289.1	n.1965+9777C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0807 AC: 12252 AN: 151892 Hom.: 1038 Cov.: 31

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0522

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0198

Gnomad OTH AF: 0.0649

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

GnomAD4 genome AF: 0.0809 AC: 12301 AN: 152010 Hom.: 1050 Cov.: 31 AF XY: 0.0809 AC XY: 6011 AN XY: 74308

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.0396

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.185

Gnomad4 SAS AF: 0.0518

Gnomad4 FIN AF: 0.0222

Gnomad4 NFE AF: 0.0198

Gnomad4 OTH AF: 0.0638

Alfa AF: 0.0319 Hom.: 293

Bravo AF: 0.0893

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7219986; hg19: chr17-53263207;