rs233100

Positions:

• 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 ENST00000426125.1(BCL10-AS1):​n.67+28588G>A variant causes a intron, non coding transcript 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 ENST00000426125.1 intron, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCL10-AS1	ENST00000426125.1	n.67+28588G>A		intron_variant, non_coding_transcript_variant		3
BCL10-AS1	ENST00000427819.5	n.181+28588G>A		intron_variant, non_coding_transcript_variant		2
BCL10-AS1	ENST00000654182.1	n.508+28588G>A		intron_variant, non_coding_transcript_variant

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;