rs10826793

Variant names:

• chr10-30369588-C-T
• rs10826793
• ENST00000340929.4:n.284G>A

Variant summary

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

The ENST00000340929.4(GOLGA2P6):​n.284G>A 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 0.273 in 559,456 control chromosomes in the GnomAD database, including 23,369 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 0.24 (5316 hom., cov: 32)
  • Exomes 𝑓: 0.28 (18053 hom.)
• Consequence: GOLGA2P6 ENST00000340929.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 5 publications found

Genes affected

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

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]

MTPAP Gene-Disease associations (from GenCC):

• mitochondrial disease

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• spastic ataxia 4

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000340929.4. 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
	GOLGA2P6	NR_120609.1		n.875G>A		non_coding_transcript_exon	Exon 2 of 12

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA2P6	ENST00000340929.4	TSL:6	n.284G>A		non_coding_transcript_exon	Exon 5 of 14
	MTPAP	ENST00000471055.1	TSL:5	n.372G>A		non_coding_transcript_exon	Exon 3 of 10
	MTPAP	ENST00000488290.5	TSL:2	n.171G>A		non_coding_transcript_exon	Exon 2 of 17

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36956 AN: 151988 Hom.: 5314 Cov.: 32

Gnomad AFR AF: 0.0947

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.0484

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.268

GnomAD4 exome AF: 0.285 AC: 116023 AN: 407348 Hom.: 18053 Cov.: 0 AF XY: 0.284 AC XY: 63992 AN XY: 225022

African (AFR) AF: 0.0916 AC: 1083 AN: 11822

American (AMR) AF: 0.225 AC: 6212 AN: 27658

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 3125 AN: 12112

East Asian (EAS) AF: 0.0461 AC: 970 AN: 21048

South Asian (SAS) AF: 0.262 AC: 14890 AN: 56778

European-Finnish (FIN) AF: 0.326 AC: 11074 AN: 33952

Middle Eastern (MID) AF: 0.277 AC: 541 AN: 1956

European-Non Finnish (NFE) AF: 0.326 AC: 72296 AN: 221430

Other (OTH) AF: 0.283 AC: 5832 AN: 20592

GnomAD4 genome AF: 0.243 AC: 36969 AN: 152108 Hom.: 5316 Cov.: 32 AF XY: 0.241 AC XY: 17893 AN XY: 74352

African (AFR) AF: 0.0945 AC: 3923 AN: 41498

American (AMR) AF: 0.254 AC: 3874 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 853 AN: 3470

East Asian (EAS) AF: 0.0483 AC: 250 AN: 5178

South Asian (SAS) AF: 0.266 AC: 1283 AN: 4820

European-Finnish (FIN) AF: 0.315 AC: 3330 AN: 10580

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22536 AN: 67970

Other (OTH) AF: 0.266 AC: 560 AN: 2106

Alfa AF: 0.279 Hom.: 3442

Bravo AF: 0.233

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.9
DANN	Benign	0.61
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10826793; hg19: chr10-30658517; COSMIC: COSV61780874;