rs503612

chr11-95130022-C-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENDOD1	NM_015036.3	c.*443C>A		3_prime_UTR_variant	2/2	ENST00000278505.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENDOD1	ENST00000278505.5	c.*443C>A		3_prime_UTR_variant	2/2	1	NM_015036.3	P1

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

Gnomad4 AFR exome AF: 0.125

Gnomad4 AMR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.393

Gnomad4 EAS exome AF: 0.583

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.458

Gnomad4 NFE exome AF: 0.353

Gnomad4 OTH exome AF: 0.389

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

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.629

Gnomad4 SAS AF: 0.360

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.436

Gnomad4 OTH AF: 0.411

Alfa AF: 0.428 Hom.: 22168

Bravo AF: 0.401

Asia WGS AF: 0.488 AC: 1696 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.4
Dann	Benign	0.45

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: rs503612; hg19: chr11-94863186;