17-10697719-T-G

Position:

• chr17-10697719-T-G

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.-18+52T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.018 in 663,208 control chromosomes in the GnomAD database, including 697 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.015 (108 hom., cov: 33)
  • Exomes 𝑓: 0.019 (589 hom.)
• Consequence: ADPRM NM_020233.5 intron
• Clinical Significance: Likely benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.38

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]

ADPRM (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 17-10697719-T-G is Benign according to our data. Variant chr17-10697719-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 1213105.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADPRM	NM_020233.5	c.-18+52T>G		intron_variant		ENST00000379774.5	NP_064618.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ADPRM	ENST00000379774.5	c.-18+52T>G		intron_variant		1	NM_020233.5	ENSP00000369099.4
ADPRM	ENST00000468843.1	n.-18+52T>G		intron_variant		1		ENSP00000431622.1
ADPRM	ENST00000527582.2	n.52+52T>G		intron_variant		2
SCO1	ENST00000582053.1	n.436+221A>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0148 AC: 2238 AN: 151714 Hom.: 101 Cov.: 33

Gnomad AFR AF: 0.00923

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0378

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0314

Gnomad FIN AF: 0.00753

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00141

Gnomad OTH AF: 0.0173

GnomAD4 exome AF: 0.0189 AC: 9670 AN: 511376 Hom.: 589 Cov.: 6 AF XY: 0.0190 AC XY: 5124 AN XY: 269950

Gnomad4 AFR exome AF: 0.0100

Gnomad4 AMR exome AF: 0.0682

Gnomad4 ASJ exome AF: 0.0137

Gnomad4 EAS exome AF: 0.163

Gnomad4 SAS exome AF: 0.0321

Gnomad4 FIN exome AF: 0.00450

Gnomad4 NFE exome AF: 0.00120

Gnomad4 OTH exome AF: 0.0172

GnomAD4 genome AF: 0.0149 AC: 2257 AN: 151832 Hom.: 108 Cov.: 33 AF XY: 0.0159 AC XY: 1183 AN XY: 74262

Gnomad4 AFR AF: 0.00926

Gnomad4 AMR AF: 0.0377

Gnomad4 ASJ AF: 0.0135

Gnomad4 EAS AF: 0.169

Gnomad4 SAS AF: 0.0315

Gnomad4 FIN AF: 0.00753

Gnomad4 NFE AF: 0.00141

Gnomad4 OTH AF: 0.0252

Alfa AF: 0.000590 Hom.: 0

Bravo AF: 0.0187

Asia WGS AF: 0.107 AC: 372 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 29, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.3
DANN	Benign	0.26

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: rs28364712; hg19: chr17-10601036;