3-110808404-G-T

Variant names:

• chr3-110808404-G-T
• rs1462309
• ENST00000803769.1:n.208+66878C>A

Variant summary

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

The ENST00000803769.1(NECTIN3-AS1):​n.208+66878C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 150,622 control chromosomes in the GnomAD database, including 29,961 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 0.57 (29961 hom., cov: 29)
• Consequence: NECTIN3-AS1 ENST00000803769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886
• Publications: 3 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NECTIN3-AS1	ENST00000803769.1	n.208+66878C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.571 AC: 85940 AN: 150502 Hom.: 29969 Cov.: 29

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.636

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.783

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.570 AC: 85925 AN: 150622 Hom.: 29961 Cov.: 29 AF XY: 0.567 AC XY: 41681 AN XY: 73450

African (AFR) AF: 0.156 AC: 6368 AN: 40826

American (AMR) AF: 0.634 AC: 9574 AN: 15090

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2400 AN: 3464

East Asian (EAS) AF: 0.393 AC: 1987 AN: 5058

South Asian (SAS) AF: 0.686 AC: 3299 AN: 4808

European-Finnish (FIN) AF: 0.683 AC: 7038 AN: 10312

Middle Eastern (MID) AF: 0.667 AC: 192 AN: 288

European-Non Finnish (NFE) AF: 0.783 AC: 53050 AN: 67768

Other (OTH) AF: 0.623 AC: 1306 AN: 2096

Alfa AF: 0.588 Hom.: 6044

Bravo AF: 0.546

Asia WGS AF: 0.527 AC: 1822 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.25
DANN	Benign	0.50
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs1462309; hg19: chr3-110527251;