rs10494112

Variant names:

• chr1-109809855-A-G
• rs10494112

Variant summary

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

The variant allele was found at a frequency of 0.172 in 152,270 control chromosomes in the GnomAD database, including 2,529 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 0.17 (2529 hom., cov: 33)
• Consequence: NDUFA5P10 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994
• Publications: 27 publications found

Genes affected

NDUFA5P10 (HGNC:48852): (NADH:ubiquinone oxidoreductase subunit A5 pseudogene 10)

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 = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NDUFA5P10		n.109809855A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26107 AN: 152152 Hom.: 2526 Cov.: 33

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.147

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.172 AC: 26126 AN: 152270 Hom.: 2529 Cov.: 33 AF XY: 0.171 AC XY: 12707 AN XY: 74440

African (AFR) AF: 0.127 AC: 5261 AN: 41550

American (AMR) AF: 0.122 AC: 1867 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 687 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5190

South Asian (SAS) AF: 0.147 AC: 709 AN: 4826

European-Finnish (FIN) AF: 0.243 AC: 2570 AN: 10592

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.210 AC: 14277 AN: 68020

Other (OTH) AF: 0.166 AC: 350 AN: 2112

Alfa AF: 0.195 Hom.: 10120

Bravo AF: 0.160

Asia WGS AF: 0.0820 AC: 288 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.9
DANN	Benign	0.48
PhyloP100		0.99

Splicing

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

Other links and lift over

dbSNP: rs10494112; hg19: chr1-110352477;