11-129916830-G-C

Variant names:

• chr11-129916830-G-C
• rs3734070
• NM_199437.2:c.2325+297C>G

Variant summary

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

The NM_199437.2(PRDM10):​c.2325+297C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 151,924 control chromosomes in the GnomAD database, including 7,188 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 0.30 (7188 hom., cov: 32)
• Consequence: PRDM10 NM_199437.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285

Genes affected

PRDM10 (HGNC:13995): (PR/SET domain 10) The protein encoded by this gene is a transcription factor that contains C2H2-type zinc-fingers. It also contains a positive regulatory domain, which has been found in several other zinc-finger transcription factors including those involved in B cell differentiation and tumor suppression. Studies of the mouse counterpart suggest that this protein may be involved in the development of the central nerve system (CNS), as well as in the pathogenesis of neuronal storage disease. Multiple alternatively spliced transcript variants encoding distinct isoforms have been observed. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRDM10	NM_199437.2	c.2325+297C>G		intron_variant	Intron 15 of 20	ENST00000360871.8	NP_955469.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRDM10	ENST00000360871.8	c.2325+297C>G		intron_variant	Intron 15 of 20	1	NM_199437.2	ENSP00000354118.3

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46278 AN: 151806 Hom.: 7191 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.305 AC: 46275 AN: 151924 Hom.: 7188 Cov.: 32 AF XY: 0.302 AC XY: 22397 AN XY: 74250

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.318

Alfa AF: 0.176 Hom.: 331

Bravo AF: 0.297

Asia WGS AF: 0.269 AC: 938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.56

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: rs3734070; hg19: chr11-129786725;