17-10697598-G-A

Position:

• chr17-10697598-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_020233.5(ADPRM):​c.-87G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0108 in 1,502,356 control chromosomes in the GnomAD database, including 1,201 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.051 (620 hom., cov: 33)
  • Exomes 𝑓: 0.0064 (581 hom.)
• Consequence: ADPRM NM_020233.5 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.238

Genes affected

ADPRM (HGNC:30925): (ADP-ribose/CDP-alcohol diphosphatase, manganese dependent) Predicted to enable 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity; manganese ion binding activity; and pyrophosphatase activity. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

SCO1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BP6: Variant 17-10697598-G-A is Benign according to our data. Variant chr17-10697598-G-A is described in ClinVar as [Benign]. Clinvar id is 1237522.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.166 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADPRM	NM_020233.5	c.-87G>A		5_prime_UTR_variant	1/4	ENST00000379774.5	NP_064618.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADPRM	ENST00000379774	c.-87G>A		5_prime_UTR_variant	1/4	1	NM_020233.5	ENSP00000369099.4
SCO1	ENST00000582053.1	n.436+342C>T		intron_variant		4
ADPRM	ENST00000468843.1	n.-87G>A		upstream_gene_variant		1		ENSP00000431622.1
ADPRM	ENST00000527582.2	n.-18G>A		upstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.0504 AC: 7667 AN: 152176 Hom.: 616 Cov.: 33

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0261

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0191

Gnomad SAS AF: 0.00228

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00107

Gnomad OTH AF: 0.0474

GnomAD4 exome AF: 0.00636 AC: 8587 AN: 1350062 Hom.: 581 Cov.: 21 AF XY: 0.00565 AC XY: 3805 AN XY: 673266

Gnomad4 AFR exome AF: 0.184

Gnomad4 AMR exome AF: 0.0126

Gnomad4 ASJ exome AF: 0.000481

Gnomad4 EAS exome AF: 0.0167

Gnomad4 SAS exome AF: 0.00180

Gnomad4 FIN exome AF: 0.0000204

Gnomad4 NFE exome AF: 0.000589

Gnomad4 OTH exome AF: 0.0148

GnomAD4 genome AF: 0.0506 AC: 7701 AN: 152294 Hom.: 620 Cov.: 33 AF XY: 0.0492 AC XY: 3663 AN XY: 74462

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.0259

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.0189

Gnomad4 SAS AF: 0.00207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00107

Gnomad4 OTH AF: 0.0478

Alfa AF: 0.0315 Hom.: 49

Bravo AF: 0.0599

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.6
DANN	Benign	0.88

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

Other links and lift over

dbSNP: rs2662938; hg19: chr17-10600915;