rs57348955

chr16-31174561-G-Achr16-31174561-G-Cchr16-31174561-G-T

Variant summary

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

The 16-31174561-G-A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 157,476 control chromosomes in the GnomAD database, including 10,493 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 0.32 (9437 hom., cov: 27)
  • Exomes 𝑓: 0.47 (1056 hom.)
• Consequence: NDUFA3P6 ENST00000571486.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.657

Genes affected

NDUFA3P6 (HGNC:45055): (NADH:ubiquinone oxidoreductase subunit A3 pseudogene 6)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NDUFA3P6	ENST00000571486.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.317 AC: 47132 AN: 148716 Hom.: 9438 Cov.: 27

Gnomad AFR AF: 0.0740

Gnomad AMI AF: 0.517

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.496

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.379

GnomAD4 exome AF: 0.473 AC: 4131 AN: 8730 Hom.: 1056 Cov.: 0 AF XY: 0.468 AC XY: 2175 AN XY: 4648

Gnomad4 AFR exome AF: 0.0765

Gnomad4 AMR exome AF: 0.463

Gnomad4 ASJ exome AF: 0.485

Gnomad4 EAS exome AF: 0.848

Gnomad4 SAS exome AF: 0.326

Gnomad4 FIN exome AF: 0.417

Gnomad4 NFE exome AF: 0.419

Gnomad4 OTH exome AF: 0.471

GnomAD4 genome AF: 0.317 AC: 47122 AN: 148746 Hom.: 9437 Cov.: 27 AF XY: 0.321 AC XY: 23210 AN XY: 72338

Gnomad4 AFR AF: 0.0739

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.496

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.378

Alfa AF: 0.364 Hom.: 3131

Bravo AF: 0.311

Asia WGS AF: 0.452 AC: 1574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.4
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs57348955; hg19: chr16-31185882;