chr10-30367853-T-G

Variant names:

• chr10-30367853-T-G
• rs34181456
• ENST00000488290.5:n.970A>C

Variant summary

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

The ENST00000488290.5(MTPAP):​n.970A>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 0.0799 in 1,378,300 control chromosomes in the GnomAD database, including 5,410 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 0.070 (525 hom., cov: 32)
  • Exomes 𝑓: 0.081 (4885 hom.)
• Consequence: MTPAP ENST00000488290.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.41
• Publications: 2 publications found

Genes affected

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]

GOLGA2P6 (HGNC:44948): (GOLGA2 pseudogene 6)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000488290.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA2P6	NR_120609.1		n.1648A>C		non_coding_transcript_exon	Exon 6 of 12

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MTPAP	ENST00000488290.5	TSL:2	n.970A>C		non_coding_transcript_exon	Exon 6 of 17
	GOLGA2P6	ENST00000340929.4	TSL:6	n.914+293A>C		intron	N/A
	MTPAP	ENST00000471055.1	TSL:5	n.1092+293A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0704 AC: 10707 AN: 152104 Hom.: 525 Cov.: 32

Gnomad AFR AF: 0.0172

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0507

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.00618

Gnomad SAS AF: 0.0817

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0994

Gnomad OTH AF: 0.0554

GnomAD4 exome AF: 0.0811 AC: 99486 AN: 1226078 Hom.: 4885 Cov.: 27 AF XY: 0.0825 AC XY: 51007 AN XY: 618592

African (AFR) AF: 0.0118 AC: 345 AN: 29176

American (AMR) AF: 0.0430 AC: 1868 AN: 43428

Ashkenazi Jewish (ASJ) AF: 0.0627 AC: 1497 AN: 23894

East Asian (EAS) AF: 0.00292 AC: 110 AN: 37632

South Asian (SAS) AF: 0.0864 AC: 7073 AN: 81818

European-Finnish (FIN) AF: 0.142 AC: 5039 AN: 35562

Middle Eastern (MID) AF: 0.0683 AC: 290 AN: 4246

European-Non Finnish (NFE) AF: 0.0863 AC: 79331 AN: 918766

Other (OTH) AF: 0.0763 AC: 3933 AN: 51556

GnomAD4 genome AF: 0.0703 AC: 10708 AN: 152222 Hom.: 525 Cov.: 32 AF XY: 0.0719 AC XY: 5352 AN XY: 74428

African (AFR) AF: 0.0171 AC: 711 AN: 41550

American (AMR) AF: 0.0507 AC: 776 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0683 AC: 237 AN: 3472

East Asian (EAS) AF: 0.00619 AC: 32 AN: 5166

South Asian (SAS) AF: 0.0824 AC: 397 AN: 4818

European-Finnish (FIN) AF: 0.152 AC: 1612 AN: 10596

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0994 AC: 6757 AN: 67998

Other (OTH) AF: 0.0553 AC: 117 AN: 2114

Alfa AF: 0.0729 Hom.: 211

Bravo AF: 0.0584

Asia WGS AF: 0.0430 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	9.6
DANN	Benign	0.81
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs34181456; hg19: chr10-30656782; COSMIC: COSV104417122;