1-85306326-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 24 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000427819.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCL10-AS1	ENST00000426125.1	TSL:3	n.67+28588G>A		intron	N/A
	BCL10-AS1	ENST00000427819.5	TSL:2	n.181+28588G>A		intron	N/A
	BCL10-AS1	ENST00000654182.1		n.508+28588G>A		intron	N/A

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

African (AFR) AF: 0.320 AC: 13275 AN: 41464

American (AMR) AF: 0.416 AC: 6353 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1692 AN: 3466

East Asian (EAS) AF: 0.515 AC: 2657 AN: 5156

South Asian (SAS) AF: 0.337 AC: 1622 AN: 4818

European-Finnish (FIN) AF: 0.480 AC: 5076 AN: 10564

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28833 AN: 67954

Other (OTH) AF: 0.419 AC: 884 AN: 2112

Alfa AF: 0.416 Hom.: 63256

Bravo AF: 0.393

Asia WGS AF: 0.442 AC: 1537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.1
DANN	Benign	0.48
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs233100; hg19: chr1-85772009;