3-110582279-T-G

Variant names:

• chr3-110582279-T-G
• rs2399332
• ENST00000803773.1:n.235-27330A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000803773.1(NECTIN3-AS1):​n.235-27330A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 151,990 control chromosomes in the GnomAD database, including 29,633 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 0.62 (29633 hom., cov: 32)
• Consequence: NECTIN3-AS1 ENST00000803773.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 17 publications found

Genes affected

NECTIN3-AS1 (HGNC:40813): (NECTIN3 antisense RNA 1)

ENSG00000304514 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803773.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NECTIN3-AS1	ENST00000803773.1		n.235-27330A>C		intron	N/A
	ENSG00000304514	ENST00000804113.1		n.135-38T>G		intron	N/A
	ENSG00000304514	ENST00000804114.1		n.135-38T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94548 AN: 151872 Hom.: 29617 Cov.: 32

Gnomad AFR AF: 0.574

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.644

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.626

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.623 AC: 94618 AN: 151990 Hom.: 29633 Cov.: 32 AF XY: 0.624 AC XY: 46329 AN XY: 74270

African (AFR) AF: 0.574 AC: 23800 AN: 41438

American (AMR) AF: 0.599 AC: 9151 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1889 AN: 3464

East Asian (EAS) AF: 0.693 AC: 3578 AN: 5160

South Asian (SAS) AF: 0.723 AC: 3490 AN: 4826

European-Finnish (FIN) AF: 0.644 AC: 6780 AN: 10534

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43823 AN: 67992

Other (OTH) AF: 0.629 AC: 1328 AN: 2110

Alfa AF: 0.631 Hom.: 24656

Bravo AF: 0.618

Asia WGS AF: 0.706 AC: 2451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	13
DANN	Benign	0.86
PhyloP100		0.31

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2399332;

hg19: chr3-110301126;