rs4450855

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-110992334-G-A
• chr3-110992334-G-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC151760	XR_007096272.1	n.483+76930C>T		intron_variant	Intron 2 of 3
LOC151760	XR_007096273.1	n.720+76930C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NECTIN3-AS1	ENST00000383686.4	n.742+76930C>T		intron_variant	Intron 2 of 3	2
NECTIN3-AS1	ENST00000474769.7	n.303+76930C>T		intron_variant	Intron 2 of 3	3
NECTIN3-AS1	ENST00000476301.6	n.525+76930C>T		intron_variant	Intron 2 of 3	4

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 v4.3

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;