chr5-37811762-A-G

Variant names:

• chr5-37811762-A-G
• rs2910709
• ENST00000637595.1:n.174A>G

Variant summary

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

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GDNF-AS1	ENST00000637595.1	n.174A>G		non_coding_transcript_exon_variant	Exon 1 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 1.00 AC: 2 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.545 AC: 22263 AN: 40814

American (AMR) AF: 0.678 AC: 10266 AN: 15148

Ashkenazi Jewish (ASJ) AF: 0.589 AC: 2041 AN: 3468

East Asian (EAS) AF: 0.649 AC: 3306 AN: 5094

South Asian (SAS) AF: 0.701 AC: 3311 AN: 4724

European-Finnish (FIN) AF: 0.655 AC: 6628 AN: 10112

Middle Eastern (MID) AF: 0.623 AC: 182 AN: 292

European-Non Finnish (NFE) AF: 0.620 AC: 41993 AN: 67690

Other (OTH) AF: 0.608 AC: 1274 AN: 2094

Alfa AF: 0.613 Hom.: 46861

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
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs2910709; hg19: chr5-37811864;