rs6693365

Variant names:

• chr1-85284032-C-G
• rs6693365
• ENST00000426125.1:n.67+6294C>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+6294C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 152,268 control chromosomes in the GnomAD database, including 48,589 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 0.80 (48589 hom., cov: 33)
• Consequence: BCL10-AS1 ENST00000426125.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 5 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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+6294C>G		intron_variant	Intron 1 of 2	3
BCL10-AS1	ENST00000427819.5	n.181+6294C>G		intron_variant	Intron 2 of 4	2
BCL10-AS1	ENST00000654182.1	n.508+6294C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.798 AC: 121341 AN: 152150 Hom.: 48557 Cov.: 33

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.749

Gnomad FIN AF: 0.809

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.786

Gnomad OTH AF: 0.801

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

GnomAD4 genome AF: 0.797 AC: 121423 AN: 152268 Hom.: 48589 Cov.: 33 AF XY: 0.796 AC XY: 59275 AN XY: 74464

African (AFR) AF: 0.845 AC: 35108 AN: 41558

American (AMR) AF: 0.756 AC: 11571 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2796 AN: 3472

East Asian (EAS) AF: 0.698 AC: 3614 AN: 5178

South Asian (SAS) AF: 0.749 AC: 3614 AN: 4828

European-Finnish (FIN) AF: 0.809 AC: 8589 AN: 10614

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.786 AC: 53425 AN: 67992

Other (OTH) AF: 0.804 AC: 1697 AN: 2112

Alfa AF: 0.794 Hom.: 5962

Bravo AF: 0.795

Asia WGS AF: 0.760 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.73
DANN	Benign	0.50
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs6693365; hg19: chr1-85749715;