11-95128682-A-G

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_015036.3(ENDOD1):ā€‹c.606A>Gā€‹(p.Thr202=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00227 in 1,614,212 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā˜…).

Frequency

Genomes: š‘“ 0.0017 ( 1 hom., cov: 32)
Exomes š‘“: 0.0023 ( 7 hom. )

Consequence

ENDOD1
NM_015036.3 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -7.42
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.96).
BP6
Variant 11-95128682-A-G is Benign according to our data. Variant chr11-95128682-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2642303.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-7.42 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 7 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ENDOD1NM_015036.3 linkuse as main transcriptc.606A>G p.Thr202= synonymous_variant 2/2 ENST00000278505.5 NP_055851.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENDOD1ENST00000278505.5 linkuse as main transcriptc.606A>G p.Thr202= synonymous_variant 2/21 NM_015036.3 ENSP00000278505 P1

Frequencies

GnomAD3 genomes
AF:
0.00166
AC:
252
AN:
152210
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000748
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000458
Gnomad ASJ
AF:
0.00490
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000188
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00285
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.00195
AC:
486
AN:
249462
Hom.:
0
AF XY:
0.00182
AC XY:
247
AN XY:
135344
show subpopulations
Gnomad AFR exome
AF:
0.000646
Gnomad AMR exome
AF:
0.000521
Gnomad ASJ exome
AF:
0.00566
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000327
Gnomad FIN exome
AF:
0.000232
Gnomad NFE exome
AF:
0.00337
Gnomad OTH exome
AF:
0.00215
GnomAD4 exome
AF:
0.00234
AC:
3417
AN:
1461884
Hom.:
7
Cov.:
34
AF XY:
0.00226
AC XY:
1646
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.000329
Gnomad4 AMR exome
AF:
0.000425
Gnomad4 ASJ exome
AF:
0.00643
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000348
Gnomad4 FIN exome
AF:
0.000468
Gnomad4 NFE exome
AF:
0.00276
Gnomad4 OTH exome
AF:
0.00195
GnomAD4 genome
AF:
0.00165
AC:
252
AN:
152328
Hom.:
1
Cov.:
32
AF XY:
0.00128
AC XY:
95
AN XY:
74492
show subpopulations
Gnomad4 AFR
AF:
0.000746
Gnomad4 AMR
AF:
0.000458
Gnomad4 ASJ
AF:
0.00490
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000188
Gnomad4 NFE
AF:
0.00285
Gnomad4 OTH
AF:
0.000473
Alfa
AF:
0.00305
Hom.:
0
Bravo
AF:
0.00172
EpiCase
AF:
0.00267
EpiControl
AF:
0.00302

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenJan 01, 2023ENDOD1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.078
DANN
Benign
0.47

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.

Other links and lift over

dbSNP: rs184606168; hg19: chr11-94861846; API