chr5-37811762-A-G

Position:

• chr5-37811762-A-G

Variant summary

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

The ENST00000637595.1(GDNF-AS1):​n.174A>G 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 0.611 in 150,344 control chromosomes in the GnomAD database, including 28,177 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 0.61 (28176 hom., cov: 28)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: GDNF-AS1 ENST00000637595.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.297

Genes affected

GDNF-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37811762A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GDNF-AS1	ENST00000637595.1	n.174A>G		non_coding_transcript_exon_variant	1/12	5

Frequencies

GnomAD3 genomes AF: 0.611 AC: 91778 AN: 150234 Hom.: 28158 Cov.: 28

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.630

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.589

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.702

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.613

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 SAS exome AF: 1.00

GnomAD4 genome AF: 0.611 AC: 91835 AN: 150342 Hom.: 28176 Cov.: 28 AF XY: 0.614 AC XY: 44950 AN XY: 73226

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.589

Gnomad4 EAS AF: 0.649

Gnomad4 SAS AF: 0.701

Gnomad4 FIN AF: 0.655

Gnomad4 NFE AF: 0.620

Gnomad4 OTH AF: 0.608

Alfa AF: 0.613 Hom.: 36507

Bravo AF: 0.608

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2910709; hg19: chr5-37811864;