rs503612

Variant names:

• chr11-95130022-C-A
• rs503612
• NM_015036.3:c.*443C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015036.3(ENDOD1):​c.*443C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.402 in 153,010 control chromosomes in the GnomAD database, including 12,881 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 (12789 hom., cov: 32)
  • Exomes 𝑓: 0.37 (92 hom.)
• Consequence: ENDOD1 NM_015036.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692
• Publications: 3 publications found

Genes affected

ENDOD1 (HGNC:29129): (endonuclease domain containing 1) Predicted to enable endonuclease activity; metal ion binding activity; and nucleic acid binding activity. Predicted to be involved in nucleic acid phosphodiester bond hydrolysis. Located in extracellular exosome and membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015036.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENDOD1	NM_015036.3	MANE Select	c.*443C>A		3_prime_UTR	Exon 2 of 2	NP_055851.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENDOD1	ENST00000278505.5	TSL:1 MANE Select	c.*443C>A		3_prime_UTR	Exon 2 of 2	ENSP00000278505.4

Frequencies

GnomAD3 genomes AF: 0.402 AC: 61087 AN: 151810 Hom.: 12777 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.406

GnomAD4 exome AF: 0.368 AC: 397 AN: 1080 Hom.: 92 Cov.: 0 AF XY: 0.363 AC XY: 197 AN XY: 542

African (AFR) AF: 0.125 AC: 2 AN: 16

American (AMR) AF: 0.500 AC: 53 AN: 106

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 11 AN: 28

East Asian (EAS) AF: 0.583 AC: 7 AN: 12

South Asian (SAS) AF: 0.250 AC: 10 AN: 40

European-Finnish (FIN) AF: 0.458 AC: 11 AN: 24

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.353 AC: 289 AN: 818

Other (OTH) AF: 0.389 AC: 14 AN: 36

GnomAD4 genome AF: 0.402 AC: 61141 AN: 151930 Hom.: 12789 Cov.: 32 AF XY: 0.406 AC XY: 30132 AN XY: 74266

African (AFR) AF: 0.284 AC: 11794 AN: 41458

American (AMR) AF: 0.462 AC: 7055 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1555 AN: 3472

East Asian (EAS) AF: 0.629 AC: 3242 AN: 5158

South Asian (SAS) AF: 0.360 AC: 1734 AN: 4818

European-Finnish (FIN) AF: 0.466 AC: 4904 AN: 10524

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29635 AN: 67932

Other (OTH) AF: 0.411 AC: 865 AN: 2104

Alfa AF: 0.424 Hom.: 53000

Bravo AF: 0.401

Asia WGS AF: 0.488 AC: 1696 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.4
DANN	Benign	0.45
PhyloP100		0.69
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs503612; hg19: chr11-94863186;