rs34672588

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The ENST00000332972.9(ADSS1):c.6G>A(p.Val2Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 787,880 control chromosomes in the GnomAD database, including 56,283 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.46 ( 15282 hom., cov: 26)

Exomes 𝑓: 0.25 ( 41001 hom. )

Consequence

ADSS1
ENST00000332972.9 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.145

Publications

6 publications found

Variant links:

Genes affected

ADSS1 (HGNC:20093): (adenylosuccinate synthase 1) This gene encodes a member of the adenylosuccinate synthase family of proteins. The encoded muscle-specific enzyme plays a role in the purine nucleotide cycle by catalyzing the first step in the conversion of inosine monophosphate (IMP) to adenosine monophosphate (AMP). Mutations in this gene may cause adolescent onset distal myopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]

ADSS1 Gene-Disease associations (from GenCC):

myopathy, distal, 5
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

ADSS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -16 ACMG points.

BP6

Variant 14-104729898-G-A is Benign according to our data. Variant chr14-104729898-G-A is described in ClinVar as Benign. ClinVar VariationId is 1189013.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000332972.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ADSS1	NM_152328.5	MANE Select	c.193-5122G>A		intron	N/A	NP_689541.1
ADSS1	NM_199165.2		c.6G>A	p.Val2Val	synonymous	Exon 1 of 13	NP_954634.1
ADSS1	NM_001320424.1		c.-722G>A		5_prime_UTR	Exon 1 of 13	NP_001307353.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ADSS1	ENST00000332972.9	TSL:1	c.6G>A	p.Val2Val	synonymous	Exon 1 of 13	ENSP00000333019.5
ADSS1	ENST00000330877.7	TSL:1 MANE Select	c.193-5122G>A		intron	N/A	ENSP00000331260.2
ADSS1	ENST00000553540.5	TSL:2	n.6G>A		non_coding_transcript_exon	Exon 1 of 13	ENSP00000450759.1

Frequencies

GnomAD3 genomes

AF:

0.458

AC:

54114

AN:

118048

Hom.:

15261

Cov.:

show subpopulations

Gnomad AFR

AF:

0.529

Gnomad AMI

AF:

0.232

Gnomad AMR

AF:

0.481

Gnomad ASJ

AF:

0.371

Gnomad EAS

AF:

0.574

Gnomad SAS

AF:

0.534

Gnomad FIN

AF:

0.426

Gnomad MID

AF:

0.375

Gnomad NFE

AF:

0.410

Gnomad OTH

AF:

0.451

GnomAD2 exomes

AF:

0.311

AC:

21025

AN:

67694

AF XY:

0.300

show subpopulations

Gnomad AFR exome

AF:

0.482

Gnomad AMR exome

AF:

0.349

Gnomad ASJ exome

AF:

0.133

Gnomad EAS exome

AF:

0.534

Gnomad FIN exome

AF:

0.206

Gnomad NFE exome

AF:

0.260

Gnomad OTH exome

AF:

0.319

GnomAD4 exome

AF:

0.253

AC:

169475

AN:

669770

Hom.:

41001

Cov.:

AF XY:

0.266

AC XY:

89409

AN XY:

336586

show subpopulations

African (AFR)

AF:

0.398

AC:

5977

AN:

15020

American (AMR)

AF:

0.393

AC:

7633

AN:

19408

Ashkenazi Jewish (ASJ)

AF:

0.284

AC:

4523

AN:

15904

East Asian (EAS)

AF:

0.480

AC:

12154

AN:

25310

South Asian (SAS)

AF:

0.437

AC:

20021

AN:

45774

European-Finnish (FIN)

AF:

0.411

AC:

13039

AN:

31692

Middle Eastern (MID)

AF:

0.295

AC:

755

AN:

2558

European-Non Finnish (NFE)

AF:

0.198

AC:

95503

AN:

482834

Other (OTH)

AF:

0.316

AC:

9870

AN:

31270

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

5032

10064

15097

20129

25161

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

522

1044

1566

2088

2610

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.459

AC:

54155

AN:

118110

Hom.:

15282

Cov.:

AF XY:

0.461

AC XY:

26178

AN XY:

56788

show subpopulations

African (AFR)

AF:

0.529

AC:

17787

AN:

33606

American (AMR)

AF:

0.482

AC:

5595

AN:

11614

Ashkenazi Jewish (ASJ)

AF:

0.371

AC:

1057

AN:

2852

East Asian (EAS)

AF:

0.572

AC:

1949

AN:

3406

South Asian (SAS)

AF:

0.533

AC:

1786

AN:

3348

European-Finnish (FIN)

AF:

0.426

AC:

3207

AN:

7534

Middle Eastern (MID)

AF:

0.357

AC:

AN:

230

European-Non Finnish (NFE)

AF:

0.410

AC:

21810

AN:

53244

Other (OTH)

AF:

0.452

AC:

728

AN:

1612

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

1176

2353

3529

4706

5882

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

438

876

1314

1752

2190

<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:

0.416

Hom.:

3562

Bravo

AF:

0.492

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

Myopathy, distal, 5

Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

3.0

(source)

DANN

Benign

0.76

PhyloP100

-0.14

PromoterAI

0.038

Neutral

(source)

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

3.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.44

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.44

Position offset: -3

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over