5-37845041-G-C

Position:

• chr5-37845041-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_145476.1(GDNF-AS1):​n.155+5003G>C variant causes a intron, non coding transcript 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 NR_145476.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GDNF-AS1	NR_145476.1	n.155+5003G>C		intron_variant, non_coding_transcript_variant
GDNF-AS1	NR_103441.2	n.136+4468G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GDNF-AS1	ENST00000503382.6	n.136+4468G>C		intron_variant, non_coding_transcript_variant		1
GDNF-AS1	ENST00000637595.1	n.1021-16220G>C		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.295

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.298

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1981844; hg19: chr5-37845143;