Variant rs6644 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_152328.5(ADSS1):c.*3A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 1,612,700 control chromosomes in the GnomAD database, including 206,508 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.61 ( 30761 hom., cov: 33)

Exomes 𝑓: 0.48 ( 175747 hom. )

Consequence

ADSS1
NM_152328.5 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.73

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 14-104747006-A-G is Benign according to our data. Variant chr14-104747006-A-G is described in ClinVar as [Benign]. Clinvar id is 1189017.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADSS1	NM_152328.5 link	c.*3A>G		3_prime_UTR_variant	13/13	ENST00000330877.7	NP_689541.1	Q8N142-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADSS1	ENST00000330877.7 link	c.*3A>G		3_prime_UTR_variant	13/13	1	NM_152328.5	ENSP00000331260.2		Q8N142-1

Frequencies

GnomAD3 genomes

AF:

0.607

AC:

92237

AN:

152036

Hom.:

30714

Cov.:

show subpopulations

Gnomad AFR

AF:

0.889

Gnomad AMI

AF:

0.333

Gnomad AMR

AF:

0.633

Gnomad ASJ

AF:

0.409

Gnomad EAS

AF:

0.633

Gnomad SAS

AF:

0.613

Gnomad FIN

AF:

0.498

Gnomad MID

AF:

0.494

Gnomad NFE

AF:

0.458

Gnomad OTH

AF:

0.583

GnomAD3 exomes

AF:

0.547

AC:

137562

AN:

251342

Hom.:

39917

AF XY:

0.534

AC XY:

72594

AN XY:

135842

show subpopulations

Gnomad AFR exome

AF:

0.895

Gnomad AMR exome

AF:

0.685

Gnomad ASJ exome

AF:

0.414

Gnomad EAS exome

AF:

0.631

Gnomad SAS exome

AF:

0.579

Gnomad FIN exome

AF:

0.500

Gnomad NFE exome

AF:

0.456

Gnomad OTH exome

AF:

0.517

GnomAD4 exome

AF:

0.482

AC:

703779

AN:

1460546

Hom.:

175747

Cov.:

AF XY:

0.482

AC XY:

350154

AN XY:

726502

show subpopulations

Gnomad4 AFR exome

AF:

0.908

Gnomad4 AMR exome

AF:

0.678

Gnomad4 ASJ exome

AF:

0.413

Gnomad4 EAS exome

AF:

0.583

Gnomad4 SAS exome

AF:

0.574

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.450

Gnomad4 OTH exome

AF:

0.508

GnomAD4 genome

AF:

0.607

AC:

92339

AN:

152154

Hom.:

30761

Cov.:

AF XY:

0.609

AC XY:

45334

AN XY:

74384

show subpopulations

Gnomad4 AFR

AF:

0.889

Gnomad4 AMR

AF:

0.634

Gnomad4 ASJ

AF:

0.409

Gnomad4 EAS

AF:

0.632

Gnomad4 SAS

AF:

0.612

Gnomad4 FIN

AF:

0.498

Gnomad4 NFE

AF:

0.458

Gnomad4 OTH

AF:

0.584

Alfa

AF:

0.499

Hom.:

25831

Bravo

AF:

0.630

Asia WGS

AF:

0.653

AC:

2272

AN:

3478

EpiCase

AF:

0.471

EpiControl

AF:

0.459

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

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.11

DANN

Benign

0.34

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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