chr1-109809855-A-G

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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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 v4.9

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;