chr13-21301957-C-G

Variant names:

• chr13-21301957-C-G
• rs9788333
• ENST00000691775.3:n.781C>G

Variant summary

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

The ENST00000691775.3(ENSG00000291046):​n.781C>G 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 0.274 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: ENSG00000291046 ENST00000691775.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.592
• Publications: 6 publications found

Genes affected

ENSG00000291046 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691775.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MIPEPP3	NR_038939.1		n.438+339C>G		intron	N/A
	MIPEPP3	NR_046461.1		n.438+339C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000291046	ENST00000691775.3		n.781C>G		non_coding_transcript_exon	Exon 2 of 2
	MIPEPP3	ENST00000412105.1	TSL:6	n.355+339C>G		intron	N/A
	ENSG00000291046	ENST00000424756.3	TSL:3	n.272+339C>G		intron	N/A

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

African (AFR) AF: 0.108 AC: 4435 AN: 41230

American (AMR) AF: 0.229 AC: 3478 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 860 AN: 3466

East Asian (EAS) AF: 0.302 AC: 1562 AN: 5166

South Asian (SAS) AF: 0.364 AC: 1742 AN: 4788

European-Finnish (FIN) AF: 0.358 AC: 3691 AN: 10320

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24725 AN: 67848

Other (OTH) AF: 0.274 AC: 577 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.9
DANN	Benign	0.52
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs9788333; hg19: chr13-21876096;