20-15668721-G-A

Position:

• chr20-15668721-G-A

Variant summary

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

The NM_001351661.2(MACROD2):​c.645+168874G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.556 in 151,940 control chromosomes in the GnomAD database, including 23,952 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 0.56 (23952 hom., cov: 32)
• Consequence: MACROD2 NM_001351661.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

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 = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MACROD2	NM_001351661.2	c.645+168874G>A		intron_variant		ENST00000684519.1	NP_001338590.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MACROD2	ENST00000684519.1	c.645+168874G>A		intron_variant			NM_001351661.2	ENSP00000507484	P2
MACROD2	ENST00000402914.5	c.-61+168874G>A		intron_variant		1		ENSP00000385290
MACROD2	ENST00000217246.8	c.645+168874G>A		intron_variant		2		ENSP00000217246	A2
MACROD2	ENST00000642719.1	c.645+168874G>A		intron_variant				ENSP00000496601	A2

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84459 AN: 151822 Hom.: 23926 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.660

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.556 AC: 84544 AN: 151940 Hom.: 23952 Cov.: 32 AF XY: 0.563 AC XY: 41833 AN XY: 74302

Gnomad4 AFR AF: 0.551

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.851

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.527

Gnomad4 OTH AF: 0.525

Alfa AF: 0.525 Hom.: 41149

Bravo AF: 0.558

Asia WGS AF: 0.730 AC: 2536 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.44

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: rs6043422; hg19: chr20-15649366; COSMIC: COSV54060727;