rs2853838

Variant names:

• chr10-47308252-A-C
• rs2853838
• NM_004962.5:c.320-1544A>C

Your query was ambiguous. Multiple possible variants found:

• chr10-47308252-A-C
• chr10-47308252-A-G
• chr10-47308252-A-T

Variant summary

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

The NM_004962.5(GDF10):​c.320-1544A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,042 control chromosomes in the GnomAD database, including 37,829 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 0.68 (37829 hom., cov: 32)
• Consequence: GDF10 NM_004962.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.188
• Publications: 10 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=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004962.5. 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
	GDF10	NM_004962.5	MANE Select	c.320-1544A>C		intron	N/A	NP_004953.1	P55107

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GDF10	ENST00000580279.2	TSL:1 MANE Select	c.320-1544A>C		intron	N/A	ENSP00000464145.1	P55107
	GDF10	ENST00000895678.1		c.320-1547A>C		intron	N/A	ENSP00000565737.1

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103744 AN: 151926 Hom.: 37823 Cov.: 32

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.775

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.683 AC: 103777 AN: 152042 Hom.: 37829 Cov.: 32 AF XY: 0.684 AC XY: 50854 AN XY: 74324

African (AFR) AF: 0.401 AC: 16609 AN: 41434

American (AMR) AF: 0.760 AC: 11606 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2788 AN: 3468

East Asian (EAS) AF: 0.776 AC: 4002 AN: 5158

South Asian (SAS) AF: 0.680 AC: 3266 AN: 4806

European-Finnish (FIN) AF: 0.821 AC: 8684 AN: 10572

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.798 AC: 54262 AN: 68018

Other (OTH) AF: 0.708 AC: 1492 AN: 2106

Alfa AF: 0.761 Hom.: 183279

Bravo AF: 0.666

Asia WGS AF: 0.687 AC: 2392 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.69
PhyloP100		-0.19

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: rs2853838; hg19: chr10-48431110;