rs6079553

chr20-14751960-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.418+67001C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,596 control chromosomes in the GnomAD database, including 13,740 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 0.40 (13740 hom., cov: 31)
• Consequence: MACROD2 NM_001351661.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392

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 (NFE) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MACROD2	NM_001351661.2	c.418+67001C>T		intron_variant		ENST00000684519.1
MACROD2	NM_001351663.2	c.418+67001C>T		intron_variant
MACROD2	NM_080676.6	c.418+67001C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MACROD2	ENST00000684519.1	c.418+67001C>T		intron_variant			NM_001351661.2	P2

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61268 AN: 151476 Hom.: 13740 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.418

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

GnomAD4 genome AF: 0.404 AC: 61269 AN: 151596 Hom.: 13740 Cov.: 31 AF XY: 0.402 AC XY: 29791 AN XY: 74096

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.152

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.574

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.413

Alfa AF: 0.470 Hom.: 7758

Bravo AF: 0.378

Asia WGS AF: 0.228 AC: 796 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	0.34
Dann	Benign	0.21

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: rs6079553; hg19: chr20-14732606;