Variant 20-14234955-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001351661.2(MACROD2):c.271+149227T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,134 control chromosomes in the GnomAD database, including 3,106 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 0.17 ( 3106 hom., cov: 32)

Consequence

MACROD2
NM_001351661.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.10

Variant links:

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]

MACROD2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.41).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
MACROD2	NM_001351661.2 link	c.271+149227T>G	intron_variant	ENST00000684519.1	NP_001338590.1
MACROD2	NM_001351663.2 link	c.271+149227T>G	intron_variant		NP_001338592.1
MACROD2	NM_080676.6 link	c.271+149227T>G	intron_variant		NP_542407.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MACROD2	ENST00000684519.1 link	c.271+149227T>G		intron_variant			NM_001351661.2	ENSP00000507484.1		A1Z1Q3-1

Frequencies

GnomAD3 genomes

AF:

0.167

AC:

25440

AN:

152016

Hom.:

3106

Cov.:

show subpopulations

Gnomad AFR

AF:

0.340

Gnomad AMI

AF:

0.0714

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.0901

Gnomad EAS

AF:

0.245

Gnomad SAS

AF:

0.130

Gnomad FIN

AF:

0.0871

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.0828

Gnomad OTH

AF:

0.162

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

GnomAD4 genome

AF:

0.167

AC:

25465

AN:

152134

Hom.:

3106

Cov.:

AF XY:

0.166

AC XY:

12317

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.339

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.0901

Gnomad4 EAS

AF:

0.245

Gnomad4 SAS

AF:

0.131

Gnomad4 FIN

AF:

0.0871

Gnomad4 NFE

AF:

0.0828

Gnomad4 OTH

AF:

0.160

Alfa

AF:

0.0711

Hom.:

136

Bravo

AF:

0.182

Asia WGS

AF:

0.187

AC:

650

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.41

CADD

Benign

DANN

Benign

0.82

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over