rs10055239

Variant names:

• chr5-38068014-C-T
• rs10055239
• ENST00000513039.3:n.332+38958C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000513039.3(GDNF-AS1):​n.332+38958C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.17 in 152,148 control chromosomes in the GnomAD database, including 2,512 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 0.17 (2512 hom., cov: 33)
• Consequence: GDNF-AS1 ENST00000513039.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.898
• Publications: 0 publications found

Genes affected

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

LINC02107 (HGNC:52962): (long intergenic non-protein coding RNA 2107)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513039.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02107	NR_147009.1		n.233+38958C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GDNF-AS1	ENST00000513039.3	TSL:3	n.332+38958C>T		intron	N/A
	GDNF-AS1	ENST00000652286.1		n.313+38958C>T		intron	N/A
	GDNF-AS1	ENST00000662564.1		n.351+26723C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.170 AC: 25845 AN: 152030 Hom.: 2502 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.0738

Gnomad EAS AF: 0.0951

Gnomad SAS AF: 0.0981

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.170 AC: 25877 AN: 152148 Hom.: 2512 Cov.: 33 AF XY: 0.173 AC XY: 12894 AN XY: 74390

African (AFR) AF: 0.236 AC: 9797 AN: 41514

American (AMR) AF: 0.106 AC: 1620 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0738 AC: 256 AN: 3470

East Asian (EAS) AF: 0.0949 AC: 491 AN: 5172

South Asian (SAS) AF: 0.0981 AC: 473 AN: 4820

European-Finnish (FIN) AF: 0.262 AC: 2778 AN: 10584

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10061 AN: 67972

Other (OTH) AF: 0.125 AC: 264 AN: 2116

Alfa AF: 0.148 Hom.: 934

Bravo AF: 0.161

Asia WGS AF: 0.0890 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.22
DANN	Benign	0.75
PhyloP100		-0.90

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10055239;

hg19: chr5-38068116;