3-110597840-C-T

Variant names:

• chr3-110597840-C-T
• rs1512532
• ENST00000803773.1:n.234+40645G>A

Variant summary

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

The ENST00000803773.1(NECTIN3-AS1):​n.234+40645G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,754 control chromosomes in the GnomAD database, including 6,463 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 0.27 (6463 hom., cov: 32)
• Consequence: NECTIN3-AS1 ENST00000803773.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.373
• Publications: 4 publications found

Genes affected

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

ENSG00000304514 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374037	XR_924328.3	n.335+40645G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NECTIN3-AS1	ENST00000803773.1	n.234+40645G>A		intron_variant	Intron 2 of 3
NECTIN3-AS1	ENST00000803774.1	n.496-9042G>A		intron_variant	Intron 5 of 5
NECTIN3-AS1	ENST00000803775.1	n.282-9099G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40459 AN: 151634 Hom.: 6462 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.267 AC: 40460 AN: 151754 Hom.: 6463 Cov.: 32 AF XY: 0.262 AC XY: 19399 AN XY: 74146

African (AFR) AF: 0.132 AC: 5473 AN: 41462

American (AMR) AF: 0.228 AC: 3479 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1613 AN: 3470

East Asian (EAS) AF: 0.0189 AC: 98 AN: 5176

South Asian (SAS) AF: 0.227 AC: 1096 AN: 4818

European-Finnish (FIN) AF: 0.292 AC: 3069 AN: 10504

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.363 AC: 24640 AN: 67798

Other (OTH) AF: 0.268 AC: 561 AN: 2096

Alfa AF: 0.344 Hom.: 10322

Bravo AF: 0.256

Asia WGS AF: 0.112 AC: 389 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	7.8
DANN	Benign	0.80
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs1512532; hg19: chr3-110316687;