20-15736556-T-TCTACTA

Variant names:

• chr20-15736556-T-TCTACTA
• rs140733
• NM_001351661.2:c.646-126189_646-126188insCTACTA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_001351661.2(MACROD2):​c.646-126189_646-126188insCTACTA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.68 (38023 hom., cov: 0)
• Consequence: MACROD2 NM_001351661.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MACROD2	NM_001351661.2	c.646-126189_646-126188insCTACTA		intron_variant	Intron 8 of 17	ENST00000684519.1	NP_001338590.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MACROD2	ENST00000684519.1	c.646-126189_646-126188insCTACTA		intron_variant	Intron 8 of 17		NM_001351661.2	ENSP00000507484.1
MACROD2	ENST00000402914.5	c.-60-126189_-60-126188insCTACTA		intron_variant	Intron 4 of 13	1		ENSP00000385290.1
MACROD2	ENST00000642719.1	c.646-126189_646-126188insCTACTA		intron_variant	Intron 8 of 17			ENSP00000496601.1
MACROD2	ENST00000217246.8	c.646-126189_646-126188insCTACTA		intron_variant	Intron 8 of 16	2		ENSP00000217246.4

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103460 AN: 151884 Hom.: 38011 Cov.: 0

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.750

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.792

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.720

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

GnomAD4 genome AF: 0.681 AC: 103498 AN: 152002 Hom.: 38023 Cov.: 0 AF XY: 0.679 AC XY: 50481 AN XY: 74322

African (AFR) AF: 0.394 AC: 16352 AN: 41450

American (AMR) AF: 0.709 AC: 10824 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.750 AC: 2600 AN: 3466

East Asian (EAS) AF: 0.505 AC: 2603 AN: 5154

South Asian (SAS) AF: 0.739 AC: 3562 AN: 4820

European-Finnish (FIN) AF: 0.831 AC: 8812 AN: 10598

Middle Eastern (MID) AF: 0.797 AC: 231 AN: 290

European-Non Finnish (NFE) AF: 0.827 AC: 56173 AN: 67944

Other (OTH) AF: 0.724 AC: 1528 AN: 2110

Alfa AF: 0.631 Hom.: 1569

Asia WGS AF: 0.644 AC: 2238 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.11
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs140733; hg19: chr20-15717201;