ENST00000513039.3:n.332+54624C>T

Variant names:

• chr5-38083680-C-T
• rs1494645
• ENST00000513039.3:n.332+54624C>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+54624C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 152,124 control chromosomes in the GnomAD database, including 1,733 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 0.15 (1733 hom., cov: 32)
• Consequence: GDNF-AS1 ENST00000513039.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 3 publications found

Genes affected

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

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

LOC105374730 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 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+54624C>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+54624C>T		intron	N/A
	GDNF-AS1	ENST00000652286.1		n.313+54624C>T		intron	N/A
	GDNF-AS1	ENST00000662564.1		n.351+42389C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22651 AN: 152006 Hom.: 1731 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.0831

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.149 AC: 22679 AN: 152124 Hom.: 1733 Cov.: 32 AF XY: 0.151 AC XY: 11211 AN XY: 74364

African (AFR) AF: 0.172 AC: 7138 AN: 41474

American (AMR) AF: 0.127 AC: 1937 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 617 AN: 3464

East Asian (EAS) AF: 0.121 AC: 623 AN: 5164

South Asian (SAS) AF: 0.0836 AC: 403 AN: 4820

European-Finnish (FIN) AF: 0.209 AC: 2215 AN: 10596

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.136 AC: 9253 AN: 68000

Other (OTH) AF: 0.128 AC: 271 AN: 2116

Alfa AF: 0.139 Hom.: 6479

Bravo AF: 0.143

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.6
DANN	Benign	0.81
PhyloP100		0.30

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: rs1494645;

hg19: chr5-38083782;