rs270545

Variant names:

• chr5-38051491-G-A
• rs270545
• ENST00000513039.3:n.332+22435G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-38051491-G-A
• chr5-38051491-G-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+22435G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,010 control chromosomes in the GnomAD database, including 6,813 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 (6813 hom., cov: 32)
• Consequence: GDNF-AS1 ENST00000513039.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.332
• Publications: 11 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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.233+22435G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GDNF-AS1	ENST00000513039.3	TSL:3	n.332+22435G>A		intron	N/A
	GDNF-AS1	ENST00000652286.1		n.313+22435G>A		intron	N/A
	GDNF-AS1	ENST00000662564.1		n.351+10200G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44528 AN: 151890 Hom.: 6798 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.293 AC: 44575 AN: 152010 Hom.: 6813 Cov.: 32 AF XY: 0.300 AC XY: 22253 AN XY: 74298

African (AFR) AF: 0.279 AC: 11562 AN: 41478

American (AMR) AF: 0.233 AC: 3561 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 845 AN: 3470

East Asian (EAS) AF: 0.327 AC: 1685 AN: 5158

South Asian (SAS) AF: 0.201 AC: 965 AN: 4802

European-Finnish (FIN) AF: 0.454 AC: 4796 AN: 10560

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20216 AN: 67956

Other (OTH) AF: 0.258 AC: 545 AN: 2116

Alfa AF: 0.289 Hom.: 12306

Bravo AF: 0.277

Asia WGS AF: 0.234 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.66
DANN	Benign	0.48
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs270545; hg19: chr5-38051593;