chr1-85278789-A-G

Variant names:

• chr1-85278789-A-G
• rs2735591
• ENST00000426125.1:n.67+1051A>G

Variant summary

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

The ENST00000426125.1(BCL10-AS1):​n.67+1051A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.726 in 152,180 control chromosomes in the GnomAD database, including 40,356 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 0.73 (40356 hom., cov: 33)
• Consequence: BCL10-AS1 ENST00000426125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.978
• Publications: 9 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 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+1051A>G		intron_variant	Intron 1 of 2	3
BCL10-AS1	ENST00000427819.5	n.181+1051A>G		intron_variant	Intron 2 of 4	2
BCL10-AS1	ENST00000654182.1	n.508+1051A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110419 AN: 152062 Hom.: 40325 Cov.: 33

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.712

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

GnomAD4 genome AF: 0.726 AC: 110498 AN: 152180 Hom.: 40356 Cov.: 33 AF XY: 0.726 AC XY: 54029 AN XY: 74410

African (AFR) AF: 0.785 AC: 32596 AN: 41528

American (AMR) AF: 0.683 AC: 10440 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.663 AC: 2302 AN: 3472

East Asian (EAS) AF: 0.699 AC: 3612 AN: 5170

South Asian (SAS) AF: 0.734 AC: 3537 AN: 4822

European-Finnish (FIN) AF: 0.720 AC: 7614 AN: 10582

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47936 AN: 68000

Other (OTH) AF: 0.716 AC: 1510 AN: 2110

Alfa AF: 0.709 Hom.: 162020

Bravo AF: 0.725

Asia WGS AF: 0.746 AC: 2597 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.2
DANN	Benign	0.90
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs2735591; hg19: chr1-85744472;