Genetic Variant DARS1-AS1:n.547+36706T>C (chr2-136035544-T-C) – 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.547+36706T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,088 control chromosomes in the GnomAD database, including 4,327 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 0.19 ( 4327 hom., cov: 32)

Consequence

DARS1-AS1
ENST00000717303.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.589

Publications

5 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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 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.547+36706T>C	intron_variant	Intron 2 of 2
DARS1-AS1	ENST00000764009.1 link	n.542+36706T>C	intron_variant	Intron 2 of 2
DARS1-AS1	ENST00000764010.1 link	n.374-42604T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.189

AC:

28739

AN:

151970

Hom.:

4313

Cov.:

show subpopulations

Gnomad AFR

AF:

0.368

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.215

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.420

Gnomad SAS

AF:

0.290

Gnomad FIN

AF:

0.111

Gnomad MID

AF:

0.182

Gnomad NFE

AF:

0.0625

Gnomad OTH

AF:

0.201

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

GnomAD4 genome

AF:

0.189

AC:

28792

AN:

152088

Hom.:

4327

Cov.:

AF XY:

0.195

AC XY:

14494

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.368

AC:

15268

AN:

41438

American (AMR)

AF:

0.215

AC:

3284

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

751

AN:

3464

East Asian (EAS)

AF:

0.420

AC:

2170

AN:

5170

South Asian (SAS)

AF:

0.290

AC:

1398

AN:

4828

European-Finnish (FIN)

AF:

0.111

AC:

1175

AN:

10586

Middle Eastern (MID)

AF:

0.178

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0626

AC:

4255

AN:

68016

Other (OTH)

AF:

0.202

AC:

427

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1029

2057

3086

4114

5143

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

288

576

864

1152

1440

<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:

0.112

Hom.:

6300

Bravo

AF:

0.207

Asia WGS

AF:

0.337

AC:

1172

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.61

(source)

DANN

Benign

0.71

PhyloP100

-0.59

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