Variant chr16-67184488-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_178516.4(EXOC3L1):c.2147G>A(p.Arg716His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00782 in 1,522,036 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0049 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0081 ( 55 hom. )

Consequence

EXOC3L1
NM_178516.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.663

Variant links:

Genes affected

EXOC3L1 (HGNC:27540): (exocyst complex component 3 like 1) Predicted to enable SNARE binding activity. Predicted to be involved in exocyst localization; exocytosis; and peptide hormone secretion. Predicted to be located in secretory granule. Predicted to be part of exocyst. [provided by Alliance of Genome Resources, Apr 2022]

EXOC3L1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00631842).

BP6

Variant 16-67184488-C-T is Benign according to our data. Variant chr16-67184488-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2646610.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 55 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EXOC3L1	NM_178516.4 linkuse as main transcript	c.2147G>A	p.Arg716His	missense_variant	14/14	ENST00000314586.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EXOC3L1	ENST00000314586.11 linkuse as main transcript	c.2147G>A	p.Arg716His	missense_variant	14/14	2	NM_178516.4	P1

Frequencies

GnomAD3 genomes

AF:

0.00493

AC:

750

AN:

152094

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00157

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00157

Gnomad ASJ

AF:

0.00317

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00290

Gnomad FIN

AF:

0.000755

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00922

Gnomad OTH

AF:

0.000478

GnomAD3 exomes

AF:

0.00538

AC:

649

AN:

120596

Hom.:

AF XY:

0.00579

AC XY:

386

AN XY:

66610

show subpopulations

Gnomad AFR exome

AF:

0.00137

Gnomad AMR exome

AF:

0.00179

Gnomad ASJ exome

AF:

0.00189

Gnomad EAS exome

AF:

0.000110

Gnomad SAS exome

AF:

0.00478

Gnomad FIN exome

AF:

0.00191

Gnomad NFE exome

AF:

0.00980

Gnomad OTH exome

AF:

0.00322

GnomAD4 exome

AF:

0.00814

AC:

11151

AN:

1369832

Hom.:

Cov.:

AF XY:

0.00812

AC XY:

5490

AN XY:

675846

show subpopulations

Gnomad4 AFR exome

AF:

0.00148

Gnomad4 AMR exome

AF:

0.00161

Gnomad4 ASJ exome

AF:

0.00209

Gnomad4 EAS exome

AF:

0.0000290

Gnomad4 SAS exome

AF:

0.00461

Gnomad4 FIN exome

AF:

0.00218

Gnomad4 NFE exome

AF:

0.00955

Gnomad4 OTH exome

AF:

0.00526

GnomAD4 genome

AF:

0.00493

AC:

751

AN:

152204

Hom.:

Cov.:

AF XY:

0.00445

AC XY:

331

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.00157

Gnomad4 AMR

AF:

0.00157

Gnomad4 ASJ

AF:

0.00317

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00311

Gnomad4 FIN

AF:

0.000755

Gnomad4 NFE

AF:

0.00922

Gnomad4 OTH

AF:

0.000473

Alfa

AF:

0.00565

Hom.:

Bravo

AF:

0.00490

TwinsUK

AF:

0.00351

AC:

ALSPAC

AF:

0.00778

AC:

ESP6500AA

AF:

0.00210

AC:

ESP6500EA

AF:

0.00590

AC:

ExAC

AF:

0.00277

AC:

130

Asia WGS

AF:

0.00203

AC:

AN:

3468

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 submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2022

EXOC3L1: BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.14

BayesDel_addAF

Benign

-0.44

BayesDel_noAF

Benign

-0.39

CADD

Benign

DANN

Uncertain

0.98

DEOGEN2

Benign

0.0062

Eigen

Uncertain

0.38

Eigen_PC

Uncertain

0.27

FATHMM_MKL

Benign

0.55

LIST_S2

Benign

0.84

MetaRNN

Benign

0.0063

MetaSVM

Benign

-1.2

MutationAssessor

Pathogenic

2.9

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.59

PROVEAN

Benign

-0.89

REVEL

Benign

0.22

Sift

Benign

0.13

Sift4G

Uncertain

0.044

Polyphen

1.0

Vest4

0.31

MVP

0.72

MPC

1.1

ClinPred

0.060

GERP RS

4.4

Varity_R

0.12

gMVP

0.66

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over