rs2735591

chr1-85278789-A-Gchr1-85278789-A-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+1051A>G 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 0.726 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.978

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=-0.8).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCL10-AS1	ENST00000426125.1	n.67+1051A>G		intron_variant, non_coding_transcript_variant		3
BCL10-AS1	ENST00000427819.5	n.181+1051A>G		intron_variant, non_coding_transcript_variant		2
BCL10-AS1	ENST00000654182.1	n.508+1051A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.699

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.716

Alfa AF: 0.707 Hom.: 77095

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2735591; hg19: chr1-85744472;