3-110611435-G-T

Variant names:

• chr3-110611435-G-T
• rs11919628
• ENST00000803773.1:n.234+27050C>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+27050C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 151,988 control chromosomes in the GnomAD database, including 2,766 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 0.16 (2766 hom., cov: 32)
• Consequence: NECTIN3-AS1 ENST00000803773.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 3 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=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000803773.1. 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	ENST00000803773.1		n.234+27050C>A		intron	N/A
	NECTIN3-AS1	ENST00000803774.1		n.496-22637C>A		intron	N/A
	NECTIN3-AS1	ENST00000803775.1		n.282-22694C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23573 AN: 151872 Hom.: 2753 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0963

Gnomad ASJ AF: 0.0978

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0842

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.155 AC: 23620 AN: 151988 Hom.: 2766 Cov.: 32 AF XY: 0.154 AC XY: 11425 AN XY: 74316

African (AFR) AF: 0.333 AC: 13822 AN: 41456

American (AMR) AF: 0.0961 AC: 1467 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0978 AC: 339 AN: 3466

East Asian (EAS) AF: 0.0930 AC: 479 AN: 5152

South Asian (SAS) AF: 0.171 AC: 824 AN: 4808

European-Finnish (FIN) AF: 0.0842 AC: 892 AN: 10596

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0803 AC: 5455 AN: 67920

Other (OTH) AF: 0.136 AC: 288 AN: 2112

Alfa AF: 0.108 Hom.: 3786

Bravo AF: 0.163

Asia WGS AF: 0.157 AC: 544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.43
DANN	Benign	0.34
PhyloP100		-0.50

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: rs11919628;

hg19: chr3-110330282;