rs6693365

Positions:

• chr1-85284032-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000426125.1(BCL10-AS1):​n.67+6294C>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 0.797 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

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=-0.97).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BCL10-AS1	ENST00000426125.1	n.67+6294C>G		intron_variant, non_coding_transcript_variant		3
BCL10-AS1	ENST00000427819.5	n.181+6294C>G		intron_variant, non_coding_transcript_variant		2
BCL10-AS1	ENST00000654182.1	n.508+6294C>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.845

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.749

Gnomad4 FIN AF: 0.809

Gnomad4 NFE AF: 0.786

Gnomad4 OTH AF: 0.804

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6693365; hg19: chr1-85749715;