Variant rs868213 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_178516.4(EXOC3L1):c.1385+3T>C variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0919 in 1,613,062 control chromosomes in the GnomAD database, including 12,459 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 0.17 ( 4291 hom., cov: 33)

Exomes 𝑓: 0.083 ( 8168 hom. )

Consequence

EXOC3L1
NM_178516.4 splice_donor_region, intron

Scores

Splicing: ADA: 0.0001752

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.464

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.427 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EXOC3L1	NM_178516.4 linkuse as main transcript	c.1385+3T>C		splice_donor_region_variant, intron_variant		ENST00000314586.11	NP_848611.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
EXOC3L1	ENST00000314586.11 linkuse as main transcript	c.1385+3T>C	splice_donor_region_variant, intron_variant	2	NM_178516.4	ENSP00000325674	P1
EXOC3L1	ENST00000545725.6 linkuse as main transcript	c.1076+3T>C	splice_donor_region_variant, intron_variant	2		ENSP00000439910
EXOC3L1	ENST00000563889.1 linkuse as main transcript	c.1091+3T>C	splice_donor_region_variant, intron_variant	2		ENSP00000455223
EXOC3L1	ENST00000564324.5 linkuse as main transcript	c.*309+3T>C	splice_donor_region_variant, intron_variant, NMD_transcript_variant	2		ENSP00000456435

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26522

AN:

152052

Hom.:

4281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.432

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.0942

Gnomad ASJ

AF:

0.0303

Gnomad EAS

AF:

0.0208

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.0728

Gnomad NFE

AF:

0.0667

Gnomad OTH

AF:

0.130

GnomAD3 exomes

AF:

0.108

AC:

27100

AN:

251068

Hom.:

2686

AF XY:

0.105

AC XY:

14204

AN XY:

135704

show subpopulations

Gnomad AFR exome

AF:

0.440

Gnomad AMR exome

AF:

0.0804

Gnomad ASJ exome

AF:

0.0353

Gnomad EAS exome

AF:

0.0178

Gnomad SAS exome

AF:

0.178

Gnomad FIN exome

AF:

0.115

Gnomad NFE exome

AF:

0.0716

Gnomad OTH exome

AF:

0.0750

GnomAD4 exome

AF:

0.0832

AC:

121596

AN:

1460892

Hom.:

8168

Cov.:

AF XY:

0.0843

AC XY:

61267

AN XY:

726714

show subpopulations

Gnomad4 AFR exome

AF:

0.440

Gnomad4 AMR exome

AF:

0.0816

Gnomad4 ASJ exome

AF:

0.0360

Gnomad4 EAS exome

AF:

0.0188

Gnomad4 SAS exome

AF:

0.168

Gnomad4 FIN exome

AF:

0.112

Gnomad4 NFE exome

AF:

0.0676

Gnomad4 OTH exome

AF:

0.0921

GnomAD4 genome

AF:

0.175

AC:

26570

AN:

152170

Hom.:

4291

Cov.:

AF XY:

0.175

AC XY:

12996

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.432

Gnomad4 AMR

AF:

0.0942

Gnomad4 ASJ

AF:

0.0303

Gnomad4 EAS

AF:

0.0208

Gnomad4 SAS

AF:

0.161

Gnomad4 FIN

AF:

0.122

Gnomad4 NFE

AF:

0.0667

Gnomad4 OTH

AF:

0.131

Alfa

AF:

0.0890

Hom.:

1889

Bravo

AF:

0.181

Asia WGS

AF:

0.132

AC:

459

AN:

3478

EpiCase

AF:

0.0674

EpiControl

AF:

0.0676

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

3.9

DANN

Benign

0.51

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00018

dbscSNV1_RF

Benign

0.018

SpliceAI score (max)

0.11

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over