16-31174561-G-A

Variant names:

• chr16-31174561-G-A
• rs57348955
• ENST00000571486.1:n.-12G>A

Variant summary

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

The ENST00000571486.1(NDUFA3P6):​n.-12G>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
• Publications: 15 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDUFA3P6	ENST00000571486.1	n.-12G>A		upstream_gene_variant		6

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

African (AFR) AF: 0.0765 AC: 13 AN: 170

American (AMR) AF: 0.463 AC: 137 AN: 296

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 133 AN: 274

East Asian (EAS) AF: 0.848 AC: 1034 AN: 1220

South Asian (SAS) AF: 0.326 AC: 214 AN: 656

European-Finnish (FIN) AF: 0.417 AC: 90 AN: 216

Middle Eastern (MID) AF: 0.538 AC: 28 AN: 52

European-Non Finnish (NFE) AF: 0.419 AC: 2191 AN: 5228

Other (OTH) AF: 0.471 AC: 291 AN: 618

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

African (AFR) AF: 0.0739 AC: 2972 AN: 40240

American (AMR) AF: 0.390 AC: 5826 AN: 14954

Ashkenazi Jewish (ASJ) AF: 0.496 AC: 1715 AN: 3460

East Asian (EAS) AF: 0.730 AC: 3698 AN: 5068

South Asian (SAS) AF: 0.330 AC: 1541 AN: 4670

European-Finnish (FIN) AF: 0.411 AC: 3972 AN: 9674

Middle Eastern (MID) AF: 0.483 AC: 139 AN: 288

European-Non Finnish (NFE) AF: 0.386 AC: 26016 AN: 67434

Other (OTH) AF: 0.378 AC: 777 AN: 2056

Alfa AF: 0.367 Hom.: 7141

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
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs57348955; hg19: chr16-31185882;