rs270584

Variant names:

• chr5-38074752-C-A
• rs270584
• ENST00000513039.3:n.332+45696C>A

Your query was ambiguous. Multiple possible variants found:

• chr5-38074752-C-A
• chr5-38074752-C-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+45696C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,068 control chromosomes in the GnomAD database, including 25,305 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 0.53 (25305 hom., cov: 32)
• Consequence: GDNF-AS1 ENST00000513039.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.260
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02107	NR_147009.1	n.233+45696C>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+45696C>A		intron_variant	Intron 2 of 2	3
GDNF-AS1	ENST00000652286.1	n.313+45696C>A		intron_variant	Intron 2 of 3
GDNF-AS1	ENST00000662564.1	n.351+33461C>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81169 AN: 151950 Hom.: 25247 Cov.: 32

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.534 AC: 81278 AN: 152068 Hom.: 25305 Cov.: 32 AF XY: 0.533 AC XY: 39617 AN XY: 74334

African (AFR) AF: 0.869 AC: 36086 AN: 41526

American (AMR) AF: 0.360 AC: 5495 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1330 AN: 3468

East Asian (EAS) AF: 0.346 AC: 1782 AN: 5156

South Asian (SAS) AF: 0.277 AC: 1335 AN: 4816

European-Finnish (FIN) AF: 0.546 AC: 5768 AN: 10566

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 27999 AN: 67938

Other (OTH) AF: 0.440 AC: 929 AN: 2112

Alfa AF: 0.433 Hom.: 20255

Bravo AF: 0.535

Asia WGS AF: 0.333 AC: 1160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.40
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs270584; hg19: chr5-38074854;