Variant 3-111145130-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001243288.2(NECTIN3):c.1139+93G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0242 in 1,350,586 control chromosomes in the GnomAD database, including 2,193 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.068 ( 807 hom., cov: 32)

Exomes 𝑓: 0.019 ( 1386 hom. )

Consequence

NECTIN3
NM_001243288.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.101

Variant links:

Genes affected

NECTIN3 (HGNC:17664): (nectin cell adhesion molecule 3) This gene encodes a member of the nectin family of proteins, which function as adhesion molecules at adherens junctions. This family member interacts with other nectin-like proteins and with afadin, a filamentous actin-binding protein involved in the regulation of directional motility, cell proliferation and survival. This gene plays a role in ocular development involving the ciliary body. Mutations in this gene are believed to result in congenital ocular defects. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

NECTIN3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 3-111145130-G-A is Benign according to our data. Variant chr3-111145130-G-A is described in ClinVar as [Benign]. Clinvar id is 1232214.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.227 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Protein	UniProt
NECTIN3	NM_001243288.2 linkuse as main transcript	c.1139+93G>A	intron_variant	NP_001230217.1	Q9NQS3-3
NECTIN3	XM_017006123.2 linkuse as main transcript	c.1301+93G>A	intron_variant	XP_016861612.1
NECTIN3	XM_017006126.2 linkuse as main transcript	c.1208+93G>A	intron_variant	XP_016861615.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NECTIN3	ENST00000493615.5 linkuse as main transcript	c.1139+93G>A		intron_variant		2		ENSP00000420579.1		Q9NQS3-3

Frequencies

GnomAD3 genomes

AF:

0.0675

AC:

10260

AN:

152082

Hom.:

805

Cov.:

show subpopulations

Gnomad AFR

AF:

0.168

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0252

Gnomad ASJ

AF:

0.00260

Gnomad EAS

AF:

0.237

Gnomad SAS

AF:

0.0337

Gnomad FIN

AF:

0.0897

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.00647

Gnomad OTH

AF:

0.0494

GnomAD4 exome

AF:

0.0187

AC:

22420

AN:

1198384

Hom.:

1386

AF XY:

0.0185

AC XY:

10987

AN XY:

594616

show subpopulations

Gnomad4 AFR exome

AF:

0.172

Gnomad4 AMR exome

AF:

0.0131

Gnomad4 ASJ exome

AF:

0.00259

Gnomad4 EAS exome

AF:

0.202

Gnomad4 SAS exome

AF:

0.0237

Gnomad4 FIN exome

AF:

0.0794

Gnomad4 NFE exome

AF:

0.00481

Gnomad4 OTH exome

AF:

0.0318

GnomAD4 genome

AF:

0.0676

AC:

10287

AN:

152202

Hom.:

807

Cov.:

AF XY:

0.0712

AC XY:

5300

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.169

Gnomad4 AMR

AF:

0.0252

Gnomad4 ASJ

AF:

0.00260

Gnomad4 EAS

AF:

0.238

Gnomad4 SAS

AF:

0.0333

Gnomad4 FIN

AF:

0.0897

Gnomad4 NFE

AF:

0.00647

Gnomad4 OTH

AF:

0.0489

Alfa

AF:

0.0380

Hom.:

Bravo

AF:

0.0668

Asia WGS

AF:

0.113

AC:

393

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.6

DANN

Benign

0.58

Splicing

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