ENST00000513039.3:n.333-54379G>A

Variant names:

• chr5-38129325-G-A
• rs4869566
• ENST00000513039.3:n.333-54379G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000513039.3(GDNF-AS1):​n.333-54379G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,184 control chromosomes in the GnomAD database, including 41,904 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 0.74 (41904 hom., cov: 34)
• Consequence: GDNF-AS1 ENST00000513039.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.48
• Publications: 1 publications found

Genes affected

GDNF-AS1 (HGNC:43592): (GDNF antisense RNA 1)

LINC02107 (HGNC:52962): (long intergenic non-protein coding RNA 2107)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513039.3. 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
	LINC02107	NR_147009.1		n.234-54379G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GDNF-AS1	ENST00000513039.3	TSL:3	n.333-54379G>A		intron	N/A
	GDNF-AS1	ENST00000652286.1		n.314-19143G>A		intron	N/A
	GDNF-AS1	ENST00000662564.1		n.352-3118G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.737 AC: 112139 AN: 152066 Hom.: 41873 Cov.: 34

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.707

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.738

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

GnomAD4 genome AF: 0.737 AC: 112224 AN: 152184 Hom.: 41904 Cov.: 34 AF XY: 0.731 AC XY: 54371 AN XY: 74398

African (AFR) AF: 0.834 AC: 34637 AN: 41508

American (AMR) AF: 0.740 AC: 11330 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.707 AC: 2455 AN: 3472

East Asian (EAS) AF: 0.500 AC: 2592 AN: 5180

South Asian (SAS) AF: 0.747 AC: 3610 AN: 4830

European-Finnish (FIN) AF: 0.623 AC: 6574 AN: 10560

Middle Eastern (MID) AF: 0.765 AC: 225 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48676 AN: 68012

Other (OTH) AF: 0.739 AC: 1560 AN: 2112

Alfa AF: 0.722 Hom.: 20278

Bravo AF: 0.747

Asia WGS AF: 0.691 AC: 2399 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
CADD	Benign	20
DANN	Benign	0.63
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs4869566; hg19: chr5-38129427;