rs270596

Variant names:

• chr5-38057626-C-T
• rs270596
• ENST00000513039.3:n.332+28570C>T

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+28570C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 151,888 control chromosomes in the GnomAD database, including 6,615 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 0.29 (6615 hom., cov: 32)
• Consequence: GDNF-AS1 ENST00000513039.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282
• Publications: 2 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02107	NR_147009.1	n.233+28570C>T		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+28570C>T		intron_variant	Intron 2 of 2	3
GDNF-AS1	ENST00000652286.1	n.313+28570C>T		intron_variant	Intron 2 of 3
GDNF-AS1	ENST00000662564.1	n.351+16335C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43844 AN: 151770 Hom.: 6602 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.289 AC: 43891 AN: 151888 Hom.: 6615 Cov.: 32 AF XY: 0.295 AC XY: 21905 AN XY: 74226

African (AFR) AF: 0.267 AC: 11070 AN: 41406

American (AMR) AF: 0.231 AC: 3516 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 844 AN: 3470

East Asian (EAS) AF: 0.312 AC: 1612 AN: 5162

South Asian (SAS) AF: 0.202 AC: 970 AN: 4808

European-Finnish (FIN) AF: 0.454 AC: 4792 AN: 10558

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20154 AN: 67920

Other (OTH) AF: 0.252 AC: 532 AN: 2108

Alfa AF: 0.285 Hom.: 3199

Bravo AF: 0.272

Asia WGS AF: 0.227 AC: 789 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	6.5
DANN	Benign	0.18
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs270596; hg19: chr5-38057728;