rs1209523

Variant names:

• chr20-22587304-C-T
• rs1209523
• ENST00000422494.2:n.*213G>A

Variant summary

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

The ENST00000422494.2(LNCNEF):​n.*213G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,062 control chromosomes in the GnomAD database, including 3,140 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 0.14 (3140 hom., cov: 32)
• Consequence: LNCNEF ENST00000422494.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.368
• Publications: 17 publications found

Genes affected

LNCNEF (HGNC:50656): (lncRNA neighboring enhancer of FOXA2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LNCNEF	NR_109883.1	n.*218G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LNCNEF	ENST00000422494.2	n.*213G>A		downstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21331 AN: 151944 Hom.: 3118 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0664

Gnomad ASJ AF: 0.0939

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0216

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0412

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.141 AC: 21392 AN: 152062 Hom.: 3140 Cov.: 32 AF XY: 0.138 AC XY: 10269 AN XY: 74336

African (AFR) AF: 0.365 AC: 15131 AN: 41400

American (AMR) AF: 0.0662 AC: 1012 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0939 AC: 326 AN: 3470

East Asian (EAS) AF: 0.190 AC: 978 AN: 5148

South Asian (SAS) AF: 0.104 AC: 502 AN: 4812

European-Finnish (FIN) AF: 0.0216 AC: 229 AN: 10606

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0412 AC: 2802 AN: 68012

Other (OTH) AF: 0.128 AC: 271 AN: 2110

Alfa AF: 0.0837 Hom.: 3774

Bravo AF: 0.156

Asia WGS AF: 0.197 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.7
DANN	Benign	0.83
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs1209523; hg19: chr20-22567942;