chr6-146864715-A-G

Variant names:

• chr6-146864715-A-G
• rs2274170
• ENST00000427394.5:n.551-3972T>C

Variant summary

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

The ENST00000427394.5(STXBP5-AS1):​n.551-3972T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,058 control chromosomes in the GnomAD database, including 19,514 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 0.51 (19514 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: STXBP5-AS1 ENST00000427394.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.95
• Publications: 3 publications found

Genes affected

STXBP5-AS1 (HGNC:44183): (STXBP5 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STXBP5-AS1	NR_034115.1	n.625-3972T>C		intron_variant	Intron 7 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STXBP5-AS1	ENST00000427394.5	n.551-3972T>C		intron_variant	Intron 7 of 10	1
STXBP5-AS1	ENST00000367477.7	n.696-3972T>C		intron_variant	Intron 8 of 10	2
STXBP5-AS1	ENST00000433308.2	n.436-3972T>C		intron_variant	Intron 6 of 9	2

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76815 AN: 151940 Hom.: 19504 Cov.: 33

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.505 AC: 76854 AN: 152058 Hom.: 19514 Cov.: 33 AF XY: 0.504 AC XY: 37444 AN XY: 74336

African (AFR) AF: 0.505 AC: 20959 AN: 41474

American (AMR) AF: 0.526 AC: 8033 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.350 AC: 1216 AN: 3472

East Asian (EAS) AF: 0.703 AC: 3629 AN: 5160

South Asian (SAS) AF: 0.472 AC: 2277 AN: 4822

European-Finnish (FIN) AF: 0.488 AC: 5156 AN: 10564

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33982 AN: 67980

Other (OTH) AF: 0.492 AC: 1038 AN: 2110

Alfa AF: 0.496 Hom.: 59772

Bravo AF: 0.510

Asia WGS AF: 0.566 AC: 1964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	17
DANN	Benign	0.88
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs2274170; hg19: chr6-147185851;