5-37845041-G-C

Variant names:

• chr5-37845041-G-C
• rs1981844
• ENST00000503382.6:n.136+4468G>C

Variant summary

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

The ENST00000503382.6(GDNF-AS1):​n.136+4468G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,056 control chromosomes in the GnomAD database, including 10,703 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 0.36 (10703 hom., cov: 32)
• Consequence: GDNF-AS1 ENST00000503382.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 5 publications found

Genes affected

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

ENSG00000305556 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 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.136+4468G>C		intron	N/A
	GDNF-AS1	NR_145476.1		n.155+5003G>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GDNF-AS1	ENST00000503382.6	TSL:1	n.136+4468G>C		intron	N/A
	GDNF-AS1	ENST00000637595.1	TSL:5	n.1021-16220G>C		intron	N/A
	GDNF-AS1	ENST00000637926.1	TSL:5	n.155+5003G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54170 AN: 151938 Hom.: 10685 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.357 AC: 54231 AN: 152056 Hom.: 10703 Cov.: 32 AF XY: 0.360 AC XY: 26753 AN XY: 74288

African (AFR) AF: 0.532 AC: 22065 AN: 41480

American (AMR) AF: 0.295 AC: 4505 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1068 AN: 3470

East Asian (EAS) AF: 0.276 AC: 1426 AN: 5166

South Asian (SAS) AF: 0.448 AC: 2157 AN: 4820

European-Finnish (FIN) AF: 0.341 AC: 3605 AN: 10562

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18380 AN: 67962

Other (OTH) AF: 0.298 AC: 628 AN: 2110

Alfa AF: 0.165 Hom.: 295

Bravo AF: 0.356

Asia WGS AF: 0.405 AC: 1407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.61
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs1981844; hg19: chr5-37845143;