rs6048209

chr20-22590445-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109883.1(LNCNEF):n.173-1034T>C variant causes a intron, non coding transcript 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 NR_109883.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LNCNEF	NR_109883.1	n.173-1034T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LNCNEF	ENST00000422494.1	n.173-1034T>C		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.0701

Gnomad4 ASJ AF: 0.0914

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.0932

Gnomad4 FIN AF: 0.0233

Gnomad4 NFE AF: 0.0406

Gnomad4 OTH AF: 0.133

Alfa AF: 0.107 Hom.: 352

Bravo AF: 0.161

Asia WGS AF: 0.172 AC: 596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.083
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6048209; hg19: chr20-22571083;