rs10512674

Variant names:

• chr5-38056651-A-C
• rs10512674
• ENST00000513039.3:n.332+27595A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-38056651-A-C
• chr5-38056651-A-G

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+27595A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,102 control chromosomes in the GnomAD database, including 3,151 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 0.20 (3151 hom., cov: 32)
• Consequence: GDNF-AS1 ENST00000513039.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 2 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02107	NR_147009.1	n.233+27595A>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GDNF-AS1	ENST00000513039.3	n.332+27595A>C		intron_variant	Intron 2 of 2	3
GDNF-AS1	ENST00000652286.1	n.313+27595A>C		intron_variant	Intron 2 of 3
GDNF-AS1	ENST00000662564.1	n.351+15360A>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30086 AN: 151984 Hom.: 3140 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.204

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.198 AC: 30125 AN: 152102 Hom.: 3151 Cov.: 32 AF XY: 0.202 AC XY: 14982 AN XY: 74340

African (AFR) AF: 0.227 AC: 9406 AN: 41506

American (AMR) AF: 0.138 AC: 2105 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3468

East Asian (EAS) AF: 0.191 AC: 986 AN: 5172

South Asian (SAS) AF: 0.137 AC: 660 AN: 4818

European-Finnish (FIN) AF: 0.281 AC: 2969 AN: 10564

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13031 AN: 67972

Other (OTH) AF: 0.162 AC: 342 AN: 2116

Alfa AF: 0.183 Hom.: 7910

Bravo AF: 0.190

Asia WGS AF: 0.140 AC: 488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.65
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs10512674; hg19: chr5-38056753;