rs6988470

Positions:

• chr8-21742957-T-C

Variant summary

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

The NM_001495.5(GFRA2):​c.794+7631A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,146 control chromosomes in the GnomAD database, including 27,422 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 0.57 (27422 hom., cov: 33)
• Consequence: GFRA2 NM_001495.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.184

Genes affected

GFRA2 (HGNC:4244): (GDNF family receptor alpha 2) Glial cell line-derived neurotrophic factor (GDNF) and neurturin (NTN) are two structurally related, potent neurotrophic factors that play key roles in the control of neuron survival and differentiation. The protein encoded by this gene is a member of the GDNF receptor family. It is a glycosylphosphatidylinositol(GPI)-linked cell surface receptor for both GDNF and NTN, and mediates activation of the RET tyrosine kinase receptor. This encoded protein acts preferentially as a receptor for NTN compared to its other family member, GDNF family receptor alpha 1. This gene is a candidate gene for RET-associated diseases. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -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 = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GFRA2	NM_001495.5	c.794+7631A>G		intron_variant		ENST00000524240.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GFRA2	ENST00000524240.6	c.794+7631A>G		intron_variant		1	NM_001495.5	P1

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86698 AN: 152028 Hom.: 27359 Cov.: 33

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.472

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.571 AC: 86808 AN: 152146 Hom.: 27422 Cov.: 33 AF XY: 0.566 AC XY: 42129 AN XY: 74376

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.472

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.534

Alfa AF: 0.547 Hom.: 5503

Bravo AF: 0.576

Asia WGS AF: 0.493 AC: 1715 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	0.63
DANN	Benign	0.54

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs6988470; hg19: chr8-21600469;