rs2213661

Positions:

• chr6-36158873-A-G

Variant summary

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

The ENST00000499560.2(BRPF3-AS1):​n.425T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,108 control chromosomes in the GnomAD database, including 8,321 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 0.31 (8317 hom., cov: 32)
  • Exomes 𝑓: 0.45 (4 hom.)
• Consequence: BRPF3-AS1 ENST00000499560.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.158

Genes affected

BRPF3-AS1 (HGNC:55591): (BRPF3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BRPF3-AS1	XR_926753.3	n.901T>C		non_coding_transcript_exon_variant	3/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BRPF3-AS1	ENST00000499560.2	n.425T>C		non_coding_transcript_exon_variant	4/4	1
BRPF3-AS1	ENST00000526611.5	n.355-11943T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47425 AN: 151950 Hom.: 8308 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.344

GnomAD4 exome AF: 0.447 AC: 17 AN: 38 Hom.: 4 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

Gnomad4 AFR exome AF: 0.00

Gnomad4 FIN exome AF: 0.472

GnomAD4 genome AF: 0.312 AC: 47432 AN: 152070 Hom.: 8317 Cov.: 32 AF XY: 0.309 AC XY: 22981 AN XY: 74342

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.305

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.269

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.401

Gnomad4 OTH AF: 0.348

Alfa AF: 0.380 Hom.: 19755

Bravo AF: 0.300

Asia WGS AF: 0.314 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2213661; hg19: chr6-36126650;