rs270592

Variant names:

• chr5-38066484-G-A
• rs270592
• ENST00000513039.3:n.332+37428G>A

Variant summary

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

The ENST00000513039.3(GDNF-AS1):​n.332+37428G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 151,946 control chromosomes in the GnomAD database, including 19,823 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 0.49 (19823 hom., cov: 33)
• Consequence: GDNF-AS1 ENST00000513039.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.466
• Publications: 3 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02107	NR_147009.1	n.233+37428G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GDNF-AS1	ENST00000513039.3	n.332+37428G>A		intron_variant	Intron 2 of 2	3
GDNF-AS1	ENST00000652286.1	n.313+37428G>A		intron_variant	Intron 2 of 3
GDNF-AS1	ENST00000662564.1	n.351+25193G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74049 AN: 151828 Hom.: 19779 Cov.: 33

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.488 AC: 74146 AN: 151946 Hom.: 19823 Cov.: 33 AF XY: 0.488 AC XY: 36252 AN XY: 74260

African (AFR) AF: 0.708 AC: 29359 AN: 41446

American (AMR) AF: 0.341 AC: 5200 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1341 AN: 3468

East Asian (EAS) AF: 0.355 AC: 1834 AN: 5172

South Asian (SAS) AF: 0.277 AC: 1338 AN: 4828

European-Finnish (FIN) AF: 0.547 AC: 5752 AN: 10520

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27912 AN: 67932

Other (OTH) AF: 0.409 AC: 861 AN: 2106

Alfa AF: 0.418 Hom.: 7274

Bravo AF: 0.482

Asia WGS AF: 0.322 AC: 1115 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.70
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs270592; hg19: chr5-38066586;