rs2075680

Positions:

• chr5-37840540-C-A
• chr5-37840540-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000503382.6(GDNF-AS1):​n.103C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 152,066 control chromosomes in the GnomAD database, including 3,620 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 0.18 (3620 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: GDNF-AS1 ENST00000503382.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.562

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GDNF-AS1	NR_145476.1	n.155+502C>A		intron_variant, non_coding_transcript_variant
GDNF-AS1	NR_103441.2	n.103C>A		non_coding_transcript_exon_variant	1/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GDNF-AS1	ENST00000503382.6	n.103C>A		non_coding_transcript_exon_variant	1/4	1
GDNF-AS1	ENST00000637595.1	n.1020+16014C>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27211 AN: 151948 Hom.: 3612 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.0844

Gnomad OTH AF: 0.147

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 18 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 16

Gnomad4 ASJ exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.179 AC: 27255 AN: 152066 Hom.: 3620 Cov.: 32 AF XY: 0.180 AC XY: 13383 AN XY: 74342

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.123

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0844

Gnomad4 OTH AF: 0.147

Alfa AF: 0.0394 Hom.: 29

Bravo AF: 0.186

Asia WGS AF: 0.233 AC: 812 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	17
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2075680; hg19: chr5-37840642;