17-10697654-G-A

Position:

• chr17-10697654-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.-31G>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 0.0119 in 1,006,200 control chromosomes in the GnomAD database, including 843 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.046 (523 hom., cov: 33)
  • Exomes 𝑓: 0.0059 (320 hom.)
• Consequence: ADPRM NM_020233.5 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.160

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=-0.78).
• BP6: Variant 17-10697654-G-A is Benign according to our data. Variant chr17-10697654-G-A is described in ClinVar as [Benign]. Clinvar id is 1240455.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADPRM	NM_020233.5	c.-31G>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.-31G>A		5_prime_UTR_variant	1/4	1	NM_020233.5	ENSP00000369099.4

Frequencies

GnomAD3 genomes AF: 0.0454 AC: 6912 AN: 152240 Hom.: 518 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0240

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00103

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.000882

Gnomad OTH AF: 0.0387

GnomAD4 exome AF: 0.00589 AC: 5033 AN: 853844 Hom.: 320 Cov.: 11 AF XY: 0.00504 AC XY: 2214 AN XY: 439584

Gnomad4 AFR exome AF: 0.166

Gnomad4 AMR exome AF: 0.0117

Gnomad4 ASJ exome AF: 0.000511

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000827

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000614

Gnomad4 OTH exome AF: 0.0142

GnomAD4 genome AF: 0.0456 AC: 6944 AN: 152356 Hom.: 523 Cov.: 33 AF XY: 0.0445 AC XY: 3318 AN XY: 74508

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.0238

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000827

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000882

Gnomad4 OTH AF: 0.0383

Alfa AF: 0.0209 Hom.: 72

Bravo AF: 0.0541

Asia WGS AF: 0.0100 AC: 36 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	-0.78
CADD	Benign	5.0
DANN	Benign	0.86

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: rs2662937; hg19: chr17-10600971;