chr17-10697803-C-T

Position:

• chr17-10697803-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_020233.5(ADPRM):​c.-18+136C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00551 in 327,180 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.038 (28 hom., cov: 33)
  • Exomes 𝑓: 0.0012 (14 hom.)
• Consequence: ADPRM NM_020233.5 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.14

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BP6: Variant 17-10697803-C-T is Benign according to our data. Variant chr17-10697803-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1223633.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ADPRM	NM_020233.5	c.-18+136C>T		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+136C>T		intron_variant		1	NM_020233.5	ENSP00000369099.4
ADPRM	ENST00000468843.1	n.-18+136C>T		intron_variant		1		ENSP00000431622.1
ADPRM	ENST00000527582.2	n.52+136C>T		intron_variant		2
SCO1	ENST00000582053.1	n.436+137G>A		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.0379 AC: 1445 AN: 38090 Hom.: 26 Cov.: 33

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0239

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00143

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000930

Gnomad OTH AF: 0.0399

GnomAD4 exome AF: 0.00120 AC: 348 AN: 289048 Hom.: 14 Cov.: 3 AF XY: 0.00110 AC XY: 169 AN XY: 153028

Gnomad4 AFR exome AF: 0.0395

Gnomad4 AMR exome AF: 0.00540

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000516

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000392

Gnomad4 OTH exome AF: 0.00312

GnomAD4 genome AF: 0.0382 AC: 1455 AN: 38132 Hom.: 28 Cov.: 33 AF XY: 0.0395 AC XY: 717 AN XY: 18172

Gnomad4 AFR AF: 0.134

Gnomad4 AMR AF: 0.0238

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00144

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000930

Gnomad4 OTH AF: 0.0395

Alfa AF: 0.00846 Hom.: 4

Bravo AF: 0.0114

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Oct 05, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.69
DANN	Benign	0.84

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: rs112720169; hg19: chr17-10601120;