3-111111899-ATGTGTGTGTG-A

Position:

• chr3-111111899-ATGTGTGTGTG-A

Variant summary

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

The NM_015480.3(NECTIN3):​c.161-105_161-96delGTGTGTGTGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0869 in 420,394 control chromosomes in the GnomAD database, including 490 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.082 (962 hom., cov: 0)
  • Exomes 𝑓: 0.087 (490 hom.)
  • Failed GnomAD Quality Control
• 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-ATGTGTGTGTG-A is Benign according to our data. Variant chr3-111111899-ATGTGTGTGTG-A is described in ClinVar as [Benign]. Clinvar id is 1239159.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NECTIN3	NM_015480.3	c.161-105_161-96delGTGTGTGTGT		intron_variant		ENST00000485303.6	NP_056295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NECTIN3	ENST00000485303.6	c.161-105_161-96delGTGTGTGTGT		intron_variant		1	NM_015480.3	ENSP00000418070.1

Frequencies

GnomAD3 genomes AF: 0.0821 AC: 12190 AN: 148436 Hom.: 956 Cov.: 0

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0327

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.0794

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0278

Gnomad OTH AF: 0.0848

GnomAD4 exome AF: 0.0869 AC: 36532 AN: 420394 Hom.: 490 AF XY: 0.0863 AC XY: 19034 AN XY: 220482

Gnomad4 AFR exome AF: 0.125

Gnomad4 AMR exome AF: 0.127

Gnomad4 ASJ exome AF: 0.0481

Gnomad4 EAS exome AF: 0.329

Gnomad4 SAS exome AF: 0.0929

Gnomad4 FIN exome AF: 0.137

Gnomad4 NFE exome AF: 0.0470

Gnomad4 OTH exome AF: 0.0888

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0822 AC: 12213 AN: 148542 Hom.: 962 Cov.: 0 AF XY: 0.0890 AC XY: 6437 AN XY: 72352

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0327

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.0784

Gnomad4 FIN AF: 0.132

Gnomad4 NFE AF: 0.0278

Gnomad4 OTH AF: 0.0841

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 20, 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;