rs1462795

Variant names:

• chr3-110973907-T-C
• rs1462795
• ENST00000383686.4:n.743-80077A>G

Variant summary

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

The ENST00000383686.4(NECTIN3-AS1):​n.743-80077A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,062 control chromosomes in the GnomAD database, including 43,874 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 (43874 hom., cov: 32)
• Consequence: NECTIN3-AS1 ENST00000383686.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.921 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NECTIN3-AS1	ENST00000383686.4	TSL:2	n.743-80077A>G		intron	N/A
	NECTIN3-AS1	ENST00000474769.7	TSL:3	n.304-80077A>G		intron	N/A
	NECTIN3-AS1	ENST00000476301.6	TSL:4	n.526-80077A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107863 AN: 151946 Hom.: 43876 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.709 AC: 107880 AN: 152062 Hom.: 43874 Cov.: 32 AF XY: 0.706 AC XY: 52525 AN XY: 74346

African (AFR) AF: 0.298 AC: 12363 AN: 41466

American (AMR) AF: 0.749 AC: 11445 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3058 AN: 3472

East Asian (EAS) AF: 0.522 AC: 2696 AN: 5160

South Asian (SAS) AF: 0.873 AC: 4208 AN: 4820

European-Finnish (FIN) AF: 0.802 AC: 8494 AN: 10590

Middle Eastern (MID) AF: 0.791 AC: 231 AN: 292

European-Non Finnish (NFE) AF: 0.927 AC: 63033 AN: 67962

Other (OTH) AF: 0.745 AC: 1570 AN: 2108

Alfa AF: 0.857 Hom.: 71241

Bravo AF: 0.685

Asia WGS AF: 0.689 AC: 2395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.69
DANN	Benign	0.64
PhyloP100		-0.61

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1462795;

hg19: chr3-110692754;