20-15253833-G-T

Position:

• chr20-15253833-G-T

Variant summary

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

The NM_001351661.2(MACROD2):​c.540+23772G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 152,106 control chromosomes in the GnomAD database, including 17,639 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 0.45 (17639 hom., cov: 33)
• Consequence: MACROD2 NM_001351661.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.42

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MACROD2	NM_001351661.2	c.540+23772G>T		intron_variant		ENST00000684519.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MACROD2	ENST00000684519.1	c.540+23772G>T		intron_variant			NM_001351661.2	P2
MACROD2	ENST00000402914.5	c.-166+23772G>T		intron_variant		1
MACROD2	ENST00000217246.8	c.540+23772G>T		intron_variant		2		A2
MACROD2	ENST00000642719.1	c.540+23772G>T		intron_variant				A2

Frequencies

GnomAD3 genomes AF: 0.454 AC: 68934 AN: 151988 Hom.: 17610 Cov.: 33

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.402

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.454 AC: 69012 AN: 152106 Hom.: 17639 Cov.: 33 AF XY: 0.441 AC XY: 32752 AN XY: 74342

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.389

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.402

Gnomad4 OTH AF: 0.475

Alfa AF: 0.409 Hom.: 26946

Bravo AF: 0.475

Asia WGS AF: 0.287 AC: 1004 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.1
DANN	Benign	0.26

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: rs6034134; hg19: chr20-15234479;