rs10511209

chr3-103241195-T-C

Variant summary

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

The ENST00000489989.1(NDUFA4P2):n.209T>C 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 0.0398 in 341,790 control chromosomes in the GnomAD database, including 921 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 0.072 (874 hom., cov: 33)
  • Exomes 𝑓: 0.014 (47 hom.)
• Consequence: NDUFA4P2 ENST00000489989.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192

Genes affected

NDUFA4P2 (HGNC:31362): (NDUFA4 pseudogene 2)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 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
NDUFA4P2	ENST00000489989.1	n.209T>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.0722 AC: 10984 AN: 152082 Hom.: 867 Cov.: 33

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0558

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.0601

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0248

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0163

Gnomad OTH AF: 0.0632

GnomAD4 exome AF: 0.0136 AC: 2570 AN: 189590 Hom.: 47 Cov.: 0 AF XY: 0.0124 AC XY: 1376 AN XY: 111344

Gnomad4 AFR exome AF: 0.114

Gnomad4 AMR exome AF: 0.0285

Gnomad4 ASJ exome AF: 0.00616

Gnomad4 EAS exome AF: 0.0281

Gnomad4 SAS exome AF: 0.00668

Gnomad4 FIN exome AF: 0.0135

Gnomad4 NFE exome AF: 0.00904

Gnomad4 OTH exome AF: 0.0153

GnomAD4 genome AF: 0.0725 AC: 11027 AN: 152200 Hom.: 874 Cov.: 33 AF XY: 0.0718 AC XY: 5344 AN XY: 74436

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.0557

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.0604

Gnomad4 SAS AF: 0.0220

Gnomad4 FIN AF: 0.0248

Gnomad4 NFE AF: 0.0163

Gnomad4 OTH AF: 0.0654

Alfa AF: 0.0486 Hom.: 81

Bravo AF: 0.0811

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
Cadd	Benign	9.3
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10511209; hg19: chr3-102960039;