rs2075680

Variant names:

• chr5-37840540-C-A
• rs2075680
• ENST00000503382.6:n.103C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GDNF-AS1	NR_103441.2	n.103C>A		non_coding_transcript_exon_variant	Exon 1 of 4
GDNF-AS1	NR_145476.1	n.155+502C>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GDNF-AS1	ENST00000503382.6	n.103C>A		non_coding_transcript_exon_variant	Exon 1 of 4	1
GDNF-AS1	ENST00000637595.1	n.1020+16014C>A		intron_variant	Intron 6 of 11	5
GDNF-AS1	ENST00000637926.1	n.155+502C>A		intron_variant	Intron 1 of 3	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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 14

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.368 AC: 15250 AN: 41464

American (AMR) AF: 0.123 AC: 1887 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 427 AN: 3468

East Asian (EAS) AF: 0.221 AC: 1130 AN: 5110

South Asian (SAS) AF: 0.222 AC: 1072 AN: 4818

European-Finnish (FIN) AF: 0.116 AC: 1235 AN: 10610

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.0844 AC: 5740 AN: 67970

Other (OTH) AF: 0.147 AC: 311 AN: 2116

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
PhyloP100		0.56
PromoterAI		-0.13	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2075680; hg19: chr5-37840642;