12-7713539-C-T

Position:

• chr12-7713539-C-T

Variant summary

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

The NM_199286.4(DPPA3):​c.83-1644C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,972 control chromosomes in the GnomAD database, including 6,602 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 0.27 (6602 hom., cov: 32)
• Consequence: DPPA3 NM_199286.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.901

Genes affected

DPPA3 (HGNC:19199): (developmental pluripotency associated 3) This gene encodes a protein that in mice may function as a maternal factor during the preimplantation stage of development. In mice, this gene may play a role in transcriptional repression, cell division, and maintenance of cell pluripotentiality. In humans, related intronless loci are located on chromosomes 14 and X. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPPA3	NM_199286.4	c.83-1644C>T		intron_variant		ENST00000345088.3	NP_954980.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPPA3	ENST00000345088.3	c.83-1644C>T		intron_variant		1	NM_199286.4	ENSP00000339250.2

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40232 AN: 151856 Hom.: 6579 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.265 AC: 40292 AN: 151972 Hom.: 6602 Cov.: 32 AF XY: 0.266 AC XY: 19787 AN XY: 74276

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.291

Alfa AF: 0.192 Hom.: 1558

Bravo AF: 0.296

Asia WGS AF: 0.275 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.62
DANN	Benign	0.82

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: rs7969455; hg19: chr12-7866135;