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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374037	XR_924328.3	n.336-27330A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NECTIN3-AS1	ENST00000803773.1	n.235-27330A>C		intron_variant	Intron 2 of 3
ENSG00000304514	ENST00000804113.1	n.135-38T>G		intron_variant	Intron 2 of 3
ENSG00000304514	ENST00000804114.1	n.135-38T>G		intron_variant	Intron 1 of 2
ENSG00000304514	ENST00000804115.1	n.149+3129T>G		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs2399332; hg19: chr3-110301126;