rs1993802

Variant names:

• chr3-110876555-C-T
• rs1993802
• ENST00000803769.1:n.133-1198G>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.133-1198G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,024 control chromosomes in the GnomAD database, including 46,875 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 0.76 (46875 hom., cov: 32)
• Consequence: NECTIN3-AS1 ENST00000803769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.894
• Publications: 4 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.917 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.133-1198G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115690 AN: 151906 Hom.: 46871 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.770

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.875

Gnomad FIN AF: 0.799

Gnomad MID AF: 0.841

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.789

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

GnomAD4 genome AF: 0.761 AC: 115732 AN: 152024 Hom.: 46875 Cov.: 32 AF XY: 0.757 AC XY: 56266 AN XY: 74332

African (AFR) AF: 0.486 AC: 20129 AN: 41414

American (AMR) AF: 0.769 AC: 11752 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3011 AN: 3470

East Asian (EAS) AF: 0.524 AC: 2697 AN: 5144

South Asian (SAS) AF: 0.876 AC: 4227 AN: 4826

European-Finnish (FIN) AF: 0.799 AC: 8449 AN: 10580

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.923 AC: 62756 AN: 67994

Other (OTH) AF: 0.792 AC: 1673 AN: 2112

Alfa AF: 0.866 Hom.: 181266

Bravo AF: 0.744

Asia WGS AF: 0.705 AC: 2452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.48
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs1993802; hg19: chr3-110595402;