rs10826793

chr10-30369588-C-T

Variant summary

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

The NR_120609.1(GOLGA2P6):n.875G>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 NR_120609.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GOLGA2P6	NR_120609.1	n.875G>A		non_coding_transcript_exon_variant	2/12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GOLGA2P6	ENST00000340929.4	n.284G>A		non_coding_transcript_exon_variant	5/14
MTPAP	ENST00000471055.1	n.372G>A		non_coding_transcript_exon_variant	3/10	5
MTPAP	ENST00000488290.5	n.171G>A		non_coding_transcript_exon_variant	2/17	2

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

Gnomad4 AFR exome AF: 0.0916

Gnomad4 AMR exome AF: 0.225

Gnomad4 ASJ exome AF: 0.258

Gnomad4 EAS exome AF: 0.0461

Gnomad4 SAS exome AF: 0.262

Gnomad4 FIN exome AF: 0.326

Gnomad4 NFE exome AF: 0.326

Gnomad4 OTH exome AF: 0.283

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

Gnomad4 AFR AF: 0.0945

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.0483

Gnomad4 SAS AF: 0.266

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.332

Gnomad4 OTH AF: 0.266

Alfa AF: 0.296 Hom.: 2337

Bravo AF: 0.233

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	7.9
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

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