ENST00000565050.5:n.598+27513G>T

Variant names:

• chr16-80463704-C-A
• rs4581712
• ENST00000565050.5:n.598+27513G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000565050.5(DYNLRB2-AS1):​n.598+27513G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,072 control chromosomes in the GnomAD database, including 4,594 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 0.23 (4594 hom., cov: 32)
• Consequence: DYNLRB2-AS1 ENST00000565050.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 13 publications found

Genes affected

DYNLRB2-AS1 (HGNC:55405): (DYNLRB2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565050.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNLRB2-AS1	NR_120307.1		n.252+64938G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DYNLRB2-AS1	ENST00000565050.5	TSL:5	n.598+27513G>T		intron	N/A
	DYNLRB2-AS1	ENST00000568776.5	TSL:4	n.252+64938G>T		intron	N/A
	DYNLRB2-AS1	ENST00000568819.5	TSL:5	n.362+28866G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34426 AN: 151954 Hom.: 4596 Cov.: 32

Gnomad AFR AF: 0.0924

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.227

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.226 AC: 34420 AN: 152072 Hom.: 4594 Cov.: 32 AF XY: 0.231 AC XY: 17195 AN XY: 74326

African (AFR) AF: 0.0922 AC: 3830 AN: 41532

American (AMR) AF: 0.227 AC: 3475 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3464

East Asian (EAS) AF: 0.427 AC: 2201 AN: 5160

South Asian (SAS) AF: 0.282 AC: 1361 AN: 4820

European-Finnish (FIN) AF: 0.309 AC: 3251 AN: 10538

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.271 AC: 18436 AN: 67952

Other (OTH) AF: 0.256 AC: 540 AN: 2106

Alfa AF: 0.258 Hom.: 16819

Bravo AF: 0.215

Asia WGS AF: 0.332 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.30
DANN	Benign	0.30
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs4581712; hg19: chr16-80497601;