3-111111899-ATGTGTG-A

Position:

• chr3-111111899-ATGTGTG-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_015480.3(NECTIN3):​c.161-101_161-96delGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.458 in 576,634 control chromosomes in the GnomAD database, including 31,280 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.52 (22339 hom., cov: 0)
  • Exomes 𝑓: 0.44 (8941 hom.)
• Consequence: NECTIN3 NM_015480.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-111111899-ATGTGTG-A is Benign according to our data. Variant chr3-111111899-ATGTGTG-A is described in ClinVar as [Benign]. Clinvar id is 1180040.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NECTIN3	NM_015480.3	c.161-101_161-96delGTGTGT		intron_variant		ENST00000485303.6	NP_056295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NECTIN3	ENST00000485303.6	c.161-101_161-96delGTGTGT		intron_variant		1	NM_015480.3	ENSP00000418070.1

Frequencies

GnomAD3 genomes AF: 0.520 AC: 77096 AN: 148338 Hom.: 22351 Cov.: 0

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.599

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.568

GnomAD4 exome AF: 0.436 AC: 186816 AN: 428188 Hom.: 8941 AF XY: 0.437 AC XY: 98207 AN XY: 224554

Gnomad4 AFR exome AF: 0.224

Gnomad4 AMR exome AF: 0.420

Gnomad4 ASJ exome AF: 0.457

Gnomad4 EAS exome AF: 0.278

Gnomad4 SAS exome AF: 0.438

Gnomad4 FIN exome AF: 0.442

Gnomad4 NFE exome AF: 0.464

Gnomad4 OTH exome AF: 0.434

GnomAD4 genome AF: 0.519 AC: 77089 AN: 148446 Hom.: 22339 Cov.: 0 AF XY: 0.514 AC XY: 37194 AN XY: 72298

Gnomad4 AFR AF: 0.240

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.599

Gnomad4 FIN AF: 0.582

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.570

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10581136; hg19: chr3-110830746;