rs9788333

chr13-21301957-C-Gchr13-21301957-C-T

Variant summary

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

The NR_046461.1(MIPEPP3):n.438+339C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 151,302 control chromosomes in the GnomAD database, including 6,648 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 (6648 hom., cov: 31)
• Consequence: MIPEPP3 NR_046461.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.592

Genes affected

MIPEPP3 (HGNC:39458): (mitochondrial intermediate peptidase pseudogene 3)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MIPEPP3	NR_046461.1	n.438+339C>G		intron_variant, non_coding_transcript_variant
MIPEPP3	NR_038939.1	n.438+339C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MIPEPP3	ENST00000412105.1	n.355+339C>G		intron_variant, non_coding_transcript_variant
	ENST00000701043.1	n.424+339C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41480 AN: 151190 Hom.: 6650 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.274 AC: 41474 AN: 151302 Hom.: 6648 Cov.: 31 AF XY: 0.275 AC XY: 20294 AN XY: 73896

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.358

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.274

Alfa AF: 0.302 Hom.: 938

Bravo AF: 0.255

Asia WGS AF: 0.297 AC: 1030 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	7.9
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9788333; hg19: chr13-21876096;