Genetic Variant DARS1-AS1:n.548-16999C>T (chr2-136061149-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000717303.1(DARS1-AS1):n.548-16999C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,064 control chromosomes in the GnomAD database, including 5,652 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 0.25 ( 5652 hom., cov: 32)

Consequence

DARS1-AS1
ENST00000717303.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.373

Publications

9 publications found

Variant links:

Genes affected

DARS1-AS1 (HGNC:40170): (DARS1 antisense RNA 1)

DARS1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
DARS1-AS1	ENST00000717303.1 link	n.548-16999C>T	intron_variant	Intron 2 of 2
DARS1-AS1	ENST00000764009.1 link	n.543-16999C>T	intron_variant	Intron 2 of 2
DARS1-AS1	ENST00000764010.1 link	n.374-16999C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.248

AC:

37609

AN:

151946

Hom.:

5648

Cov.:

show subpopulations

Gnomad AFR

AF:

0.136

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.417

Gnomad ASJ

AF:

0.501

Gnomad EAS

AF:

0.267

Gnomad SAS

AF:

0.348

Gnomad FIN

AF:

0.238

Gnomad MID

AF:

0.551

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.340

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

GnomAD4 genome

AF:

0.247

AC:

37617

AN:

152064

Hom.:

5652

Cov.:

AF XY:

0.255

AC XY:

18930

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.136

AC:

5631

AN:

41490

American (AMR)

AF:

0.417

AC:

6376

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.501

AC:

1741

AN:

3472

East Asian (EAS)

AF:

0.267

AC:

1382

AN:

5174

South Asian (SAS)

AF:

0.348

AC:

1672

AN:

4808

European-Finnish (FIN)

AF:

0.238

AC:

2515

AN:

10548

Middle Eastern (MID)

AF:

0.544

AC:

160

AN:

294

European-Non Finnish (NFE)

AF:

0.253

AC:

17219

AN:

67986

Other (OTH)

AF:

0.344

AC:

722

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1361

2723

4084

5446

6807

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

378

756

1134

1512

1890

<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:

0.259

Hom.:

4285

Bravo

AF:

0.253

Asia WGS

AF:

0.344

AC:

1194

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

CADD

Benign

7.2

(source)

DANN

Benign

0.61

PhyloP100

0.37

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