rs6079395

chr20-14347253-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.272-146226G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,902 control chromosomes in the GnomAD database, including 18,674 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 0.49 (18674 hom., cov: 31)
• Consequence: MACROD2 NM_001351661.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MACROD2	NM_001351661.2	c.272-146226G>A		intron_variant		ENST00000684519.1
MACROD2	NM_001351663.2	c.272-146226G>A		intron_variant
MACROD2	NM_080676.6	c.272-146226G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MACROD2	ENST00000684519.1	c.272-146226G>A		intron_variant			NM_001351661.2	P2

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74110 AN: 151784 Hom.: 18653 Cov.: 31

Gnomad AFR AF: 0.439

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.488 AC: 74189 AN: 151902 Hom.: 18674 Cov.: 31 AF XY: 0.486 AC XY: 36092 AN XY: 74258

Gnomad4 AFR AF: 0.439

Gnomad4 AMR AF: 0.455

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.477

Alfa AF: 0.515 Hom.: 45466

Bravo AF: 0.479

Asia WGS AF: 0.294 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.21
Dann	Benign	0.18

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: rs6079395; hg19: chr20-14327899;