chr6-146990505-G-A

Variant names:

• chr6-146990505-G-A
• rs10499244
• ENST00000427394.5:n.524+10936C>T

Variant summary

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

The ENST00000427394.5(STXBP5-AS1):​n.524+10936C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0395 in 152,142 control chromosomes in the GnomAD database, including 152 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 0.039 (152 hom., cov: 31)
• Consequence: STXBP5-AS1 ENST00000427394.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STXBP5-AS1	NR_034115.1	n.598+10936C>T		intron_variant	Intron 6 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STXBP5-AS1	ENST00000427394.5	n.524+10936C>T		intron_variant	Intron 6 of 10	1
STXBP5-AS1	ENST00000367477.7	n.669+10936C>T		intron_variant	Intron 7 of 10	2
STXBP5-AS1	ENST00000431143.5	n.328+10936C>T		intron_variant	Intron 4 of 6	3

Frequencies

GnomAD3 genomes AF: 0.0395 AC: 6001 AN: 152024 Hom.: 152 Cov.: 31

Gnomad AFR AF: 0.0250

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0231

Gnomad ASJ AF: 0.0487

Gnomad EAS AF: 0.0744

Gnomad SAS AF: 0.0453

Gnomad FIN AF: 0.0758

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0427

Gnomad OTH AF: 0.0412

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

GnomAD4 genome AF: 0.0395 AC: 6007 AN: 152142 Hom.: 152 Cov.: 31 AF XY: 0.0400 AC XY: 2978 AN XY: 74362

African (AFR) AF: 0.0251 AC: 1043 AN: 41534

American (AMR) AF: 0.0231 AC: 353 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0487 AC: 169 AN: 3468

East Asian (EAS) AF: 0.0746 AC: 385 AN: 5162

South Asian (SAS) AF: 0.0445 AC: 214 AN: 4810

European-Finnish (FIN) AF: 0.0758 AC: 802 AN: 10574

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0427 AC: 2903 AN: 67996

Other (OTH) AF: 0.0422 AC: 89 AN: 2110

Alfa AF: 0.0405 Hom.: 181

Bravo AF: 0.0352

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.26
DANN	Benign	0.56
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs10499244; hg19: chr6-147311641;