Genetic Variant ENST00000419808.5:n.342-4288G>A (chr2-135994399-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000419808.5(DARS1-AS1):n.342-4288G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0217 in 151,818 control chromosomes in the GnomAD database, including 139 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 0.022 ( 139 hom., cov: 32)

Consequence

DARS1-AS1
ENST00000419808.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.179

Publications

1 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DARS1-AS1	NR_110199.1 link	n.342-4288G>A		intron_variant	Intron 1 of 3
DARS1-AS1	NR_110200.1 link	n.342-4288G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
DARS1-AS1	ENST00000419808.5 link	n.342-4288G>A	intron_variant	Intron 1 of 3	5
DARS1-AS1	ENST00000438432.7 link	n.388-4288G>A	intron_variant	Intron 1 of 3	3
DARS1-AS1	ENST00000446492.1 link	n.44-4288G>A	intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.0218

AC:

3306

AN:

151700

Hom.:

139

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00383

Gnomad AMI

AF:

0.0253

Gnomad AMR

AF:

0.0732

Gnomad ASJ

AF:

0.0225

Gnomad EAS

AF:

0.0843

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.0104

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.00819

Gnomad OTH

AF:

0.0335

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

GnomAD4 genome

AF:

0.0217

AC:

3298

AN:

151818

Hom.:

139

Cov.:

AF XY:

0.0261

AC XY:

1939

AN XY:

74172

show subpopulations

African (AFR)

AF:

0.00382

AC:

158

AN:

41368

American (AMR)

AF:

0.0730

AC:

1110

AN:

15206

Ashkenazi Jewish (ASJ)

AF:

0.0225

AC:

AN:

3470

East Asian (EAS)

AF:

0.0849

AC:

440

AN:

5184

South Asian (SAS)

AF:

0.154

AC:

740

AN:

4806

European-Finnish (FIN)

AF:

0.0104

AC:

109

AN:

10490

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00821

AC:

558

AN:

67980

Other (OTH)

AF:

0.0336

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

156

312

468

624

780

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

138

184

230

<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:

0.0128

Hom.:

Bravo

AF:

0.0214

Asia WGS

AF:

0.121

AC:

420

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.95

(source)

DANN

Benign

0.70

PhyloP100

-0.18

Mutation Taster

=100/0

polymorphism (auto)

(source)

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