Genetic Variant ENST00000717303.1:n.547+36008G>A (chr2-136034846-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 ENST00000717303.1(DARS1-AS1):n.547+36008G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0959 in 151,980 control chromosomes in the GnomAD database, including 1,681 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 0.096 ( 1681 hom., cov: 32)

Consequence

DARS1-AS1
ENST00000717303.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0590

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=-0.86).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.266 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+36008G>A	intron_variant	Intron 2 of 2
DARS1-AS1	ENST00000764009.1 link	n.542+36008G>A	intron_variant	Intron 2 of 2
DARS1-AS1	ENST00000764010.1 link	n.374-43302G>A	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0957

AC:

14533

AN:

151862

Hom.:

1675

Cov.:

show subpopulations

Gnomad AFR

AF:

0.270

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0498

Gnomad ASJ

AF:

0.0599

Gnomad EAS

AF:

0.121

Gnomad SAS

AF:

0.0373

Gnomad FIN

AF:

0.0234

Gnomad MID

AF:

0.0573

Gnomad NFE

AF:

0.0175

Gnomad OTH

AF:

0.0842

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

GnomAD4 genome

AF:

0.0959

AC:

14569

AN:

151980

Hom.:

1681

Cov.:

AF XY:

0.0948

AC XY:

7042

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.270

AC:

11172

AN:

41392

American (AMR)

AF:

0.0497

AC:

758

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.0599

AC:

208

AN:

3470

East Asian (EAS)

AF:

0.120

AC:

623

AN:

5172

South Asian (SAS)

AF:

0.0369

AC:

178

AN:

4826

European-Finnish (FIN)

AF:

0.0234

AC:

247

AN:

10578

Middle Eastern (MID)

AF:

0.0582

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0175

AC:

1189

AN:

67978

Other (OTH)

AF:

0.0843

AC:

177

AN:

2100

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

542

1084

1627

2169

2711

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

142

284

426

568

710

<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:

0.0726

Hom.:

172

Bravo

AF:

0.108

Asia WGS

AF:

0.0820

AC:

285

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

3.0

(source)

DANN

Benign

0.45

PhyloP100

0.059

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