chr3-110992334-G-A

Variant names:

• chr3-110992334-G-A
• rs4450855
• ENST00000383686.4:n.742+76930C>T

Variant summary

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

The ENST00000383686.4(NECTIN3-AS1):​n.742+76930C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.715 in 151,756 control chromosomes in the GnomAD database, including 44,064 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 0.71 (44064 hom., cov: 31)
• Consequence: NECTIN3-AS1 ENST00000383686.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 3 publications found

Genes affected

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

LOC151760 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000383686.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NECTIN3-AS1	ENST00000383686.4	TSL:2	n.742+76930C>T		intron	N/A
	NECTIN3-AS1	ENST00000474769.7	TSL:3	n.303+76930C>T		intron	N/A
	NECTIN3-AS1	ENST00000476301.6	TSL:4	n.525+76930C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.715 AC: 108454 AN: 151638 Hom.: 44064 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.803

Gnomad MID AF: 0.800

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.715 AC: 108476 AN: 151756 Hom.: 44064 Cov.: 31 AF XY: 0.711 AC XY: 52753 AN XY: 74154

African (AFR) AF: 0.316 AC: 13046 AN: 41346

American (AMR) AF: 0.749 AC: 11423 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3056 AN: 3470

East Asian (EAS) AF: 0.525 AC: 2692 AN: 5126

South Asian (SAS) AF: 0.873 AC: 4215 AN: 4830

European-Finnish (FIN) AF: 0.803 AC: 8414 AN: 10482

Middle Eastern (MID) AF: 0.802 AC: 231 AN: 288

European-Non Finnish (NFE) AF: 0.928 AC: 63040 AN: 67954

Other (OTH) AF: 0.749 AC: 1579 AN: 2108

Alfa AF: 0.853 Hom.: 146368

Bravo AF: 0.690

Asia WGS AF: 0.696 AC: 2401 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.49
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs4450855; hg19: chr3-110711181;