rs6048209

Variant names:

• chr20-22590445-A-G
• rs6048209
• ENST00000422494.2:n.512-1034T>C

Variant summary

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

The ENST00000422494.2(LNCNEF):​n.512-1034T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,182 control chromosomes in the GnomAD database, including 3,479 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 0.15 (3479 hom., cov: 33)
• Consequence: LNCNEF ENST00000422494.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000422494.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCNEF	NR_109883.1		n.173-1034T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LNCNEF	ENST00000422494.2	TSL:3	n.512-1034T>C		intron	N/A
	LNCNEF	ENST00000797275.1		n.507-1034T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22163 AN: 152064 Hom.: 3458 Cov.: 33

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0703

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0939

Gnomad FIN AF: 0.0233

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0406

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.146 AC: 22224 AN: 152182 Hom.: 3479 Cov.: 33 AF XY: 0.142 AC XY: 10586 AN XY: 74406

African (AFR) AF: 0.390 AC: 16153 AN: 41454

American (AMR) AF: 0.0701 AC: 1072 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 317 AN: 3468

East Asian (EAS) AF: 0.157 AC: 812 AN: 5182

South Asian (SAS) AF: 0.0932 AC: 450 AN: 4830

European-Finnish (FIN) AF: 0.0233 AC: 247 AN: 10606

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0406 AC: 2761 AN: 68022

Other (OTH) AF: 0.133 AC: 282 AN: 2116

Alfa AF: 0.205 Hom.: 1424

Bravo AF: 0.161

Asia WGS AF: 0.172 AC: 596 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	0.083
DANN	Benign	0.34
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6048209; hg19: chr20-22571083;