rs724820

Positions:

• chr20-15086761-C-A
• chr20-15086761-C-G
• chr20-15086761-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001351661.2(MACROD2):​c.419-143179C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,890 control chromosomes in the GnomAD database, including 11,903 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 0.39 (11903 hom., cov: 32)
• Consequence: MACROD2 NM_001351661.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

Genes affected

MACROD2 (HGNC:16126): (mono-ADP ribosylhydrolase 2) The protein encoded by this gene is a deacetylase involved in removing ADP-ribose from mono-ADP-ribosylated proteins. The encoded protein has been shown to translocate from the nucleus to the cytoplasm upon DNA damage. [provided by RefSeq, May 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MACROD2	NM_001351661.2	c.419-143179C>A		intron_variant		ENST00000684519.1
MACROD2	NM_001351663.2	c.419-143179C>A		intron_variant
MACROD2	NM_080676.6	c.419-143179C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MACROD2	ENST00000684519.1	c.419-143179C>A		intron_variant			NM_001351661.2	P2
MACROD2	ENST00000217246.8	c.419-143179C>A		intron_variant		2		A2
MACROD2	ENST00000642719.1	c.419-143179C>A		intron_variant				A2

Frequencies

GnomAD3 genomes AF: 0.389 AC: 58980 AN: 151772 Hom.: 11883 Cov.: 32

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.536

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.389 AC: 59056 AN: 151890 Hom.: 11903 Cov.: 32 AF XY: 0.391 AC XY: 29030 AN XY: 74232

Gnomad4 AFR AF: 0.462

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.536

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.396

Alfa AF: 0.332 Hom.: 7895

Bravo AF: 0.399

Asia WGS AF: 0.501 AC: 1744 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
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: rs724820; hg19: chr20-15067407;