19-53224029-A-G

Position:

• chr19-53224029-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000596415.1(NDUFV2P1):​n.851T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.375 in 1,597,982 control chromosomes in the GnomAD database, including 119,199 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 0.33 (9322 hom., cov: 32)
  • Exomes 𝑓: 0.38 (109877 hom.)
• Consequence: NDUFV2P1 ENST00000596415.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.79

Genes affected

NDUFV2P1 (HGNC:7718): (NADH:ubiquinone oxidoreductase core subunit V2 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NDUFV2P1		n.53224029A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NDUFV2P1	ENST00000596415.1	n.851T>C		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.329 AC: 50050 AN: 151910 Hom.: 9323 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.519

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.317

GnomAD4 exome AF: 0.380 AC: 549098 AN: 1445954 Hom.: 109877 Cov.: 33 AF XY: 0.383 AC XY: 276064 AN XY: 720142

Gnomad4 AFR exome AF: 0.184

Gnomad4 AMR exome AF: 0.359

Gnomad4 ASJ exome AF: 0.441

Gnomad4 EAS exome AF: 0.747

Gnomad4 SAS exome AF: 0.492

Gnomad4 FIN exome AF: 0.297

Gnomad4 NFE exome AF: 0.367

Gnomad4 OTH exome AF: 0.384

GnomAD4 genome AF: 0.329 AC: 50073 AN: 152028 Hom.: 9322 Cov.: 32 AF XY: 0.332 AC XY: 24649 AN XY: 74292

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.351

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.735

Gnomad4 SAS AF: 0.519

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.323

Alfa AF: 0.345 Hom.: 1897

Bravo AF: 0.331

Asia WGS AF: 0.606 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	16
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11084227; hg19: chr19-53727282;