rs66881456

chr20-15991056-CA-Cchr20-15991056-C-CAchr20-15991056-C-CAA

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001351661.2(MACROD2):c.1153+3907del variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.56 (24537 hom., cov: 0)
• Consequence: MACROD2 NM_001351661.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.179

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 -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MACROD2	NM_001351661.2	c.1153+3907del		intron_variant		ENST00000684519.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MACROD2	ENST00000684519.1	c.1153+3907del		intron_variant			NM_001351661.2	P2

Frequencies

GnomAD3 genomes AF: 0.562 AC: 84911 AN: 151112 Hom.: 24542 Cov.: 0

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.788

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.617

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.562 AC: 84937 AN: 151228 Hom.: 24537 Cov.: 0 AF XY: 0.560 AC XY: 41368 AN XY: 73868

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.615

Gnomad4 EAS AF: 0.627

Gnomad4 SAS AF: 0.435

Gnomad4 FIN AF: 0.626

Gnomad4 NFE AF: 0.617

Gnomad4 OTH AF: 0.564

Alfa AF: 0.491 Hom.: 929

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs11482051; hg19: chr20-15971701;