chr10-30357169-T-C

Position:

• chr10-30357169-T-C

Variant summary

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

The ENST00000512082.1(DNM1P17):​n.230T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 624,258 control chromosomes in the GnomAD database, including 70,316 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 0.41 (15646 hom., cov: 32)
  • Exomes 𝑓: 0.46 (54670 hom.)
• Consequence: DNM1P17 ENST00000512082.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.16

Genes affected

DNM1P17 (HGNC:21134): (dynamin 1 pseudogene 17)

MTPAP (HGNC:25532): (mitochondrial poly(A) polymerase) The protein encoded by this gene is a member of the DNA polymerase type-B-like family. This enzyme synthesizes the 3' poly(A) tail of mitochondrial transcripts and plays a role in replication-dependent histone mRNA degradation.[provided by RefSeq, Jan 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DNM1P17	ENST00000512082.1	n.230T>C		non_coding_transcript_exon_variant	3/3
MTPAP	ENST00000488290.5	n.1912+7537A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62656 AN: 151978 Hom.: 15643 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.457

GnomAD4 exome AF: 0.459 AC: 216814 AN: 472160 Hom.: 54670 Cov.: 0 AF XY: 0.463 AC XY: 120640 AN XY: 260538

Gnomad4 AFR exome AF: 0.108

Gnomad4 AMR exome AF: 0.543

Gnomad4 ASJ exome AF: 0.485

Gnomad4 EAS exome AF: 0.119

Gnomad4 SAS exome AF: 0.429

Gnomad4 FIN exome AF: 0.457

Gnomad4 NFE exome AF: 0.511

Gnomad4 OTH exome AF: 0.459

GnomAD4 genome AF: 0.412 AC: 62660 AN: 152098 Hom.: 15646 Cov.: 32 AF XY: 0.411 AC XY: 30565 AN XY: 74356

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.452

Alfa AF: 0.486 Hom.: 2474

Bravo AF: 0.404

Asia WGS AF: 0.287 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	14
DANN	Benign	0.24

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs915230; hg19: chr10-30646098;