rs10461985

Variant names:

• chr5-37874307-G-A
• rs10461985
• ENST00000503382.6:n.410+41G>A

Variant summary

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

The ENST00000503382.6(GDNF-AS1):​n.410+41G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 151,508 control chromosomes in the GnomAD database, including 1,160 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 0.12 (1160 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: GDNF-AS1 ENST00000503382.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521
• Publications: 2 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503382.6. 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
	GDNF-AS1	NR_103441.2		n.410+41G>A		intron	N/A
	GDNF-AS1	NR_145476.1		n.429+41G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GDNF-AS1	ENST00000503382.6	TSL:1	n.410+41G>A		intron	N/A
	GDNF-AS1	ENST00000510986.2	TSL:1	n.842+41G>A		intron	N/A
	GDNF-AS1	ENST00000514532.3	TSL:1	n.2719+41G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.120 AC: 18192 AN: 151394 Hom.: 1158 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.156

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0917

Gnomad OTH AF: 0.105

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

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: 0.120 AC: 18208 AN: 151508 Hom.: 1160 Cov.: 32 AF XY: 0.124 AC XY: 9164 AN XY: 73986

African (AFR) AF: 0.154 AC: 6334 AN: 41230

American (AMR) AF: 0.104 AC: 1584 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3462

East Asian (EAS) AF: 0.156 AC: 805 AN: 5150

South Asian (SAS) AF: 0.191 AC: 911 AN: 4782

European-Finnish (FIN) AF: 0.146 AC: 1517 AN: 10412

Middle Eastern (MID) AF: 0.0890 AC: 26 AN: 292

European-Non Finnish (NFE) AF: 0.0917 AC: 6232 AN: 67940

Other (OTH) AF: 0.105 AC: 221 AN: 2098

Alfa AF: 0.104 Hom.: 2458

Bravo AF: 0.118

Asia WGS AF: 0.187 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.7
DANN	Benign	0.82
PhyloP100		0.52

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: rs10461985;

hg19: chr5-37874409;