rs1902724

Variant names:

• chr10-47301215-C-A
• rs1902724
• NM_004962.5:c.319+245C>A

Variant summary

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

The NM_004962.5(GDF10):​c.319+245C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.566 in 152,174 control chromosomes in the GnomAD database, including 27,149 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 (27149 hom., cov: 34)
• Consequence: GDF10 NM_004962.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• Publications: 6 publications found

Genes affected

GDF10 (HGNC:4215): (growth differentiation factor 10) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. This promotes neural repair after stroke. Additionally, this protein may act as a tumor suppressor and reduced expression of this gene is associated with oral cancer. [provided by RefSeq, Jul 2016]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GDF10	NM_004962.5	c.319+245C>A		intron_variant	Intron 1 of 2	ENST00000580279.2	NP_004953.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GDF10	ENST00000580279.2	c.319+245C>A		intron_variant	Intron 1 of 2	1	NM_004962.5	ENSP00000464145.1

Frequencies

GnomAD3 genomes AF: 0.567 AC: 86165 AN: 152056 Hom.: 27145 Cov.: 34

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.649

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.755

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.566 AC: 86192 AN: 152174 Hom.: 27149 Cov.: 34 AF XY: 0.570 AC XY: 42418 AN XY: 74414

African (AFR) AF: 0.268 AC: 11135 AN: 41522

American (AMR) AF: 0.660 AC: 10100 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.649 AC: 2253 AN: 3470

East Asian (EAS) AF: 0.598 AC: 3088 AN: 5168

South Asian (SAS) AF: 0.548 AC: 2645 AN: 4826

European-Finnish (FIN) AF: 0.755 AC: 7998 AN: 10596

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46814 AN: 67982

Other (OTH) AF: 0.582 AC: 1230 AN: 2112

Alfa AF: 0.601 Hom.: 37748

Bravo AF: 0.547

Asia WGS AF: 0.536 AC: 1863 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.52
PhyloP100		0.11

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: rs1902724; hg19: chr10-48438147;