rs2975100

Positions:

• chr5-37840943-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503382.6(GDNF-AS1):​n.136+370G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,206 control chromosomes in the GnomAD database, including 1,273 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 0.12 (1273 hom., cov: 32)
• Consequence: GDNF-AS1 ENST00000503382.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.19

Genes affected

GDNF-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GDNF-AS1	NR_103441.2	n.136+370G>A		intron_variant
GDNF-AS1	NR_145476.1	n.155+905G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GDNF-AS1	ENST00000503382.6	n.136+370G>A		intron_variant		1
GDNF-AS1	ENST00000637595.1	n.1020+16417G>A		intron_variant		5
GDNF-AS1	ENST00000637926.1	n.155+905G>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18451 AN: 152088 Hom.: 1270 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.121 AC: 18458 AN: 152206 Hom.: 1273 Cov.: 32 AF XY: 0.125 AC XY: 9269 AN XY: 74414

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.0836

Gnomad4 OTH AF: 0.107

Alfa AF: 0.0926 Hom.: 815

Bravo AF: 0.121

Asia WGS AF: 0.217 AC: 754 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	14
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2975100; hg19: chr5-37841045;