rs3767703

chr1-36090157-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
ADPRS	NM_017825.3	c.211+1042C>T		intron_variant		ENST00000373178.5
ADPRS	XM_011541636.3	c.-155+1042C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ADPRS	ENST00000373178.5	c.211+1042C>T		intron_variant		1	NM_017825.3	P1

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

Gnomad4 AFR AF: 0.0169

Gnomad4 AMR AF: 0.0829

Gnomad4 ASJ AF: 0.0888

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.0783

Gnomad4 NFE AF: 0.0746

Gnomad4 OTH AF: 0.0700

Alfa AF: 0.0788 Hom.: 1084

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

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: rs3767703; hg19: chr1-36555758;