rs10485772

Variant names:

• chr20-14384281-C-T
• rs10485772
• NM_001351661.2:c.272-109198C>T

Variant summary

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

The NM_001351661.2(MACROD2):​c.272-109198C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 151,986 control chromosomes in the GnomAD database, including 1,113 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 0.11 (1113 hom., cov: 33)
• Consequence: MACROD2 NM_001351661.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234
• Publications: 7 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• 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
MACROD2	NM_001351661.2	c.272-109198C>T		intron_variant	Intron 3 of 17	ENST00000684519.1	NP_001338590.1
MACROD2	NM_001351663.2	c.272-109198C>T		intron_variant	Intron 3 of 17		NP_001338592.1
MACROD2	NM_080676.6	c.272-109198C>T		intron_variant	Intron 3 of 16		NP_542407.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MACROD2	ENST00000684519.1	c.272-109198C>T		intron_variant	Intron 3 of 17		NM_001351661.2	ENSP00000507484.1

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16614 AN: 151868 Hom.: 1114 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.0853

Gnomad ASJ AF: 0.0533

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.0913

Gnomad FIN AF: 0.0744

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0714

Gnomad OTH AF: 0.0967

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

GnomAD4 genome AF: 0.109 AC: 16616 AN: 151986 Hom.: 1113 Cov.: 33 AF XY: 0.109 AC XY: 8085 AN XY: 74270

African (AFR) AF: 0.184 AC: 7646 AN: 41480

American (AMR) AF: 0.0856 AC: 1308 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0533 AC: 185 AN: 3470

East Asian (EAS) AF: 0.213 AC: 1101 AN: 5176

South Asian (SAS) AF: 0.0914 AC: 441 AN: 4824

European-Finnish (FIN) AF: 0.0744 AC: 783 AN: 10530

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0714 AC: 4847 AN: 67908

Other (OTH) AF: 0.0953 AC: 201 AN: 2110

Alfa AF: 0.0855 Hom.: 2419

Bravo AF: 0.113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.76
PhyloP100		-0.23
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: rs10485772; hg19: chr20-14364927;