Variant chr14-104729898-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The ENST00000332972.9(ADSS1):c.6G>A(p.Val2=) 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:2

Conservation

PhyloP100: -0.145

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ADSS1	NM_152328.5 linkuse as main transcript	c.193-5122G>A		intron_variant		ENST00000330877.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADSS1	ENST00000330877.7 linkuse as main transcript	c.193-5122G>A		intron_variant		1	NM_152328.5	P1	Q8N142-1

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

GnomAD3 exomes

AF:

0.311

AC:

21025

AN:

67694

Hom.:

6156

AF XY:

0.300

AC XY:

10537

AN XY:

35104

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 SAS exome

AF:

0.298

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

Gnomad4 AFR exome

AF:

0.398

Gnomad4 AMR exome

AF:

0.393

Gnomad4 ASJ exome

AF:

0.284

Gnomad4 EAS exome

AF:

0.480

Gnomad4 SAS exome

AF:

0.437

Gnomad4 FIN exome

AF:

0.411

Gnomad4 NFE exome

AF:

0.198

Gnomad4 OTH exome

AF:

0.316

GnomAD4 genome

AF:

0.459

AC:

54155

AN:

118110

Hom.:

15282

Cov.:

AF XY:

0.461

AC XY:

26178

AN XY:

56788

show subpopulations

Gnomad4 AFR

AF:

0.529

Gnomad4 AMR

AF:

0.482

Gnomad4 ASJ

AF:

0.371

Gnomad4 EAS

AF:

0.572

Gnomad4 SAS

AF:

0.533

Gnomad4 FIN

AF:

0.426

Gnomad4 NFE

AF:

0.410

Gnomad4 OTH

AF:

0.452

Alfa

AF:

0.398

Hom.:

2372

Bravo

AF:

0.492

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Myopathy, distal, 5

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

3.0

DANN

Benign

0.76

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

3.5

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over