ENST00000499560.2:n.425T>C

Variant names:

• chr6-36158873-A-G
• rs2213661
• ENST00000499560.2:n.425T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499560.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRPF3-AS1	NR_187146.1		n.1327T>C		non_coding_transcript_exon	Exon 3 of 3
	BRPF3-AS1	NR_187147.1		n.1259-11943T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BRPF3-AS1	ENST00000499560.2	TSL:1	n.425T>C		non_coding_transcript_exon	Exon 4 of 4
	BRPF3-AS1	ENST00000816544.1		n.160T>C		non_coding_transcript_exon	Exon 2 of 3
	BRPF3-AS1	ENST00000816548.1		n.239T>C		non_coding_transcript_exon	Exon 3 of 4

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

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.472 AC: 17 AN: 36

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.160 AC: 6645 AN: 41498

American (AMR) AF: 0.305 AC: 4653 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1185 AN: 3472

East Asian (EAS) AF: 0.239 AC: 1237 AN: 5178

South Asian (SAS) AF: 0.269 AC: 1301 AN: 4828

European-Finnish (FIN) AF: 0.380 AC: 4000 AN: 10530

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.401 AC: 27259 AN: 67984

Other (OTH) AF: 0.348 AC: 733 AN: 2106

Alfa AF: 0.370 Hom.: 42981

Bravo AF: 0.300

Asia WGS AF: 0.314 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.7
DANN	Benign	0.46
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs2213661; hg19: chr6-36126650;