chr17-10697743-G-C

Position:

• chr17-10697743-G-C

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+76G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0175 in 606,558 control chromosomes in the GnomAD database, including 711 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.047 (530 hom., cov: 33)
  • Exomes 𝑓: 0.0078 (181 hom.)
• Consequence: ADPRM NM_020233.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.321

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=-0.79).
• BP6: Variant 17-10697743-G-C is Benign according to our data. Variant chr17-10697743-G-C is described in ClinVar as [Benign]. Clinvar id is 1272930.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADPRM	NM_020233.5	c.-18+76G>C		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+76G>C		intron_variant		1	NM_020233.5	ENSP00000369099.4
ADPRM	ENST00000468843.1	n.-18+76G>C		intron_variant		1		ENSP00000431622.1
ADPRM	ENST00000527582.2	n.52+76G>C		intron_variant		2
SCO1	ENST00000582053.1	n.436+197C>G		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0464 AC: 7056 AN: 152154 Hom.: 525 Cov.: 33

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0239

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.0191

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.00101

Gnomad OTH AF: 0.0407

GnomAD4 exome AF: 0.00778 AC: 3535 AN: 454288 Hom.: 181 Cov.: 5 AF XY: 0.00678 AC XY: 1626 AN XY: 239948

Gnomad4 AFR exome AF: 0.163

Gnomad4 AMR exome AF: 0.0138

Gnomad4 ASJ exome AF: 0.000520

Gnomad4 EAS exome AF: 0.0164

Gnomad4 SAS exome AF: 0.00215

Gnomad4 FIN exome AF: 0.0000353

Gnomad4 NFE exome AF: 0.000779

Gnomad4 OTH exome AF: 0.0158

GnomAD4 genome AF: 0.0466 AC: 7089 AN: 152270 Hom.: 530 Cov.: 33 AF XY: 0.0458 AC XY: 3407 AN XY: 74464

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.0237

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.0189

Gnomad4 SAS AF: 0.00186

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00101

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.000954 Hom.: 2

Bravo AF: 0.0598

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	-0.79
CADD	Benign	5.0
DANN	Benign	0.41

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: rs2662936; hg19: chr17-10601060;