rs233100

Variant names:

• chr1-85306326-G-A
• rs233100
• ENST00000426125.1:n.67+28588G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-85306326-G-A
• chr1-85306326-G-C
• chr1-85306326-G-T

Variant summary

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

The ENST00000427819.5(BCL10-AS1):​n.181+28588G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,012 control chromosomes in the GnomAD database, including 12,485 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 0.40 (12485 hom., cov: 32)
• Consequence: BCL10-AS1 ENST00000427819.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157

Genes affected

BCL10-AS1 (HGNC:55868): (BCL10 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
BCL10-AS1	ENST00000426125.1	n.67+28588G>A		intron_variant	Intron 1 of 2	3
BCL10-AS1	ENST00000427819.5	n.181+28588G>A		intron_variant	Intron 2 of 4	2
BCL10-AS1	ENST00000654182.1	n.508+28588G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60803 AN: 151894 Hom.: 12484 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.400 AC: 60822 AN: 152012 Hom.: 12485 Cov.: 32 AF XY: 0.404 AC XY: 30000 AN XY: 74312

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.515

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.419

Alfa AF: 0.422 Hom.: 30296

Bravo AF: 0.393

Asia WGS AF: 0.442 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs233100; hg19: chr1-85772009;