rs3767703

Variant names:

• chr1-36090157-C-T
• rs3767703
• NM_017825.3:c.211+1042C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017825.3(ADPRS):​c.211+1042C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0694 in 152,136 control chromosomes in the GnomAD database, including 532 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.069 (532 hom., cov: 32)
• Consequence: ADPRS NM_017825.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 9 publications found

Genes affected

ADPRS (HGNC:21304): (ADP-ribosylserine hydrolase) This gene encodes a member of the ADP-ribosylglycohydrolase family. The encoded enzyme catalyzes the removal of ADP-ribose from ADP-ribosylated proteins. This enzyme localizes to the mitochondria, in addition to the nucleus and cytoplasm.[provided by RefSeq, Feb 2009]

ADPRS Gene-Disease associations (from GenCC):

• neurodegeneration, childhood-onset, stress-induced, with variable ataxia and seizures

  Inheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ADPRS	NM_017825.3	c.211+1042C>T		intron_variant	Intron 1 of 5	ENST00000373178.5	NP_060295.1
ADPRS	XM_011541636.3	c.-155+1042C>T		intron_variant	Intron 1 of 4		XP_011539938.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ADPRS	ENST00000373178.5	c.211+1042C>T		intron_variant	Intron 1 of 5	1	NM_017825.3	ENSP00000362273.4

Frequencies

GnomAD3 genomes AF: 0.0695 AC: 10571 AN: 152018 Hom.: 533 Cov.: 32

Gnomad AFR AF: 0.0170

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.0888

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.0783

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.0688

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0694 AC: 10564 AN: 152136 Hom.: 532 Cov.: 32 AF XY: 0.0741 AC XY: 5510 AN XY: 74382

African (AFR) AF: 0.0169 AC: 702 AN: 41508

American (AMR) AF: 0.0829 AC: 1266 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0888 AC: 308 AN: 3468

East Asian (EAS) AF: 0.212 AC: 1094 AN: 5152

South Asian (SAS) AF: 0.206 AC: 992 AN: 4824

European-Finnish (FIN) AF: 0.0783 AC: 829 AN: 10590

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0746 AC: 5072 AN: 67998

Other (OTH) AF: 0.0700 AC: 148 AN: 2114

Alfa AF: 0.0759 Hom.: 1697

Bravo AF: 0.0652

Asia WGS AF: 0.185 AC: 642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.52
PhyloP100		-0.31
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3767703; hg19: chr1-36555758;