Genetic Variant DYNLRB2-AS1:n.598+72874T>C (chr16-80418343-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000565050.5(DYNLRB2-AS1):n.598+72874T>C variant causes a intron change. The variant allele was found at a frequency of 0.332 in 149,034 control chromosomes in the GnomAD database, including 9,800 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 0.33 ( 9800 hom., cov: 32)

Consequence

DYNLRB2-AS1
ENST00000565050.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.64

Publications

3 publications found

Variant links:

Genes affected

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

DYNLRB2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.31).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DYNLRB2-AS1	NR_120307.1 link	n.252+110299T>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DYNLRB2-AS1	ENST00000565050.5 link	n.598+72874T>C	intron_variant	Intron 3 of 4	5
DYNLRB2-AS1	ENST00000568776.5 link	n.252+110299T>C	intron_variant	Intron 2 of 5	4
DYNLRB2-AS1	ENST00000568819.5 link	n.362+74227T>C	intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.332

AC:

49513

AN:

148914

Hom.:

9804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.557

Gnomad AMR

AF:

0.299

Gnomad ASJ

AF:

0.344

Gnomad EAS

AF:

0.373

Gnomad SAS

AF:

0.248

Gnomad FIN

AF:

0.416

Gnomad MID

AF:

0.441

Gnomad NFE

AF:

0.466

Gnomad OTH

AF:

0.362

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

GnomAD4 genome

AF:

0.332

AC:

49512

AN:

149034

Hom.:

9800

Cov.:

AF XY:

0.330

AC XY:

24070

AN XY:

72888

show subpopulations

African (AFR)

AF:

0.106

AC:

4375

AN:

41164

American (AMR)

AF:

0.298

AC:

4497

AN:

15088

Ashkenazi Jewish (ASJ)

AF:

0.344

AC:

1163

AN:

3382

East Asian (EAS)

AF:

0.374

AC:

1932

AN:

5164

South Asian (SAS)

AF:

0.249

AC:

1193

AN:

4788

European-Finnish (FIN)

AF:

0.416

AC:

4294

AN:

10310

Middle Eastern (MID)

AF:

0.429

AC:

121

AN:

282

European-Non Finnish (NFE)

AF:

0.466

AC:

30695

AN:

65894

Other (OTH)

AF:

0.360

AC:

747

AN:

2074

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1550

3099

4649

6198

7748

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

466

932

1398

1864

2330

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.410

Hom.:

16984

Bravo

AF:

0.309

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.31

CADD

Benign

(source)

DANN

Benign

0.84

PhyloP100

3.6

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over