11-27214514-C-G

Variant names:

• chr11-27214514-C-G
• rs10501081
• ENST00000525302.5:n.231+2803G>C

Variant summary

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

The ENST00000525302.5(BBOX1-AS1):​n.231+2803G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 151,998 control chromosomes in the GnomAD database, including 1,834 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 0.15 (1834 hom., cov: 31)
• Consequence: BBOX1-AS1 ENST00000525302.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540
• Publications: 1 publications found

Genes affected

BBOX1-AS1 (HGNC:50700): (BBOX1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525302.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BBOX1-AS1	NR_125766.1		n.591+2803G>C		intron	N/A
	BBOX1-AS1	NR_125767.1		n.231+2803G>C		intron	N/A
	BBOX1-AS1	NR_125768.1		n.274+2803G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BBOX1-AS1	ENST00000525302.5	TSL:4	n.231+2803G>C		intron	N/A
	BBOX1-AS1	ENST00000526061.6	TSL:4	n.241+2803G>C		intron	N/A
	BBOX1-AS1	ENST00000530430.1	TSL:4	n.564+2803G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22367 AN: 151880 Hom.: 1829 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.147 AC: 22403 AN: 151998 Hom.: 1834 Cov.: 31 AF XY: 0.148 AC XY: 10974 AN XY: 74310

African (AFR) AF: 0.176 AC: 7301 AN: 41430

American (AMR) AF: 0.107 AC: 1633 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 784 AN: 3470

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5168

South Asian (SAS) AF: 0.0903 AC: 434 AN: 4808

European-Finnish (FIN) AF: 0.200 AC: 2110 AN: 10536

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9606 AN: 67978

Other (OTH) AF: 0.154 AC: 325 AN: 2112

Alfa AF: 0.0545 Hom.: 67

Bravo AF: 0.143

Asia WGS AF: 0.0560 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.0
DANN	Benign	0.55
PhyloP100		0.054

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10501081;

hg19: chr11-27236061;