rs7096877

Variant names:

• chr10-116232128-G-A
• rs7096877
• NM_005264.8:c.419-20483C>T

Variant summary

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

The NM_005264.8(GFRA1):​c.419-20483C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,000 control chromosomes in the GnomAD database, including 9,804 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 0.35 (9804 hom., cov: 32)
• Consequence: GFRA1 NM_005264.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.649
• Publications: 1 publications found

Genes affected

GFRA1 (HGNC:4243): (GDNF family receptor alpha 1) This gene encodes a member of the glial cell line-derived neurotrophic factor receptor (GDNFR) family of proteins. The encoded preproprotein is proteolytically processed to generate the mature receptor. 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. This receptor is a glycosylphosphatidylinositol (GPI)-linked cell surface receptor for both GDNF and NTN, and mediates activation of the RET tyrosine kinase receptor. This gene is a candidate gene for Hirschsprung disease. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed. [provided by RefSeq, Jan 2016]

GFRA1 Gene-Disease associations (from GenCC):

• renal hypodysplasia/aplasia 4

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics

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 (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GFRA1	NM_005264.8	c.419-20483C>T		intron_variant	Intron 4 of 10	ENST00000355422.11	NP_005255.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GFRA1	ENST00000355422.11	c.419-20483C>T		intron_variant	Intron 4 of 10	5	NM_005264.8	ENSP00000347591.6

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53339 AN: 151880 Hom.: 9788 Cov.: 32

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.283

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.351 AC: 53392 AN: 152000 Hom.: 9804 Cov.: 32 AF XY: 0.352 AC XY: 26128 AN XY: 74310

African (AFR) AF: 0.447 AC: 18534 AN: 41440

American (AMR) AF: 0.317 AC: 4846 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1404 AN: 3466

East Asian (EAS) AF: 0.286 AC: 1477 AN: 5164

South Asian (SAS) AF: 0.441 AC: 2127 AN: 4822

European-Finnish (FIN) AF: 0.308 AC: 3260 AN: 10568

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20600 AN: 67936

Other (OTH) AF: 0.370 AC: 782 AN: 2114

Alfa AF: 0.326 Hom.: 1011

Bravo AF: 0.354

Asia WGS AF: 0.411 AC: 1429 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.94
DANN	Benign	0.40
PhyloP100		-0.65
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7096877; hg19: chr10-117991640;