19-53224029-A-G

Variant names:

• chr19-53224029-A-G
• rs11084227
• ENST00000596415.1:n.851T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

Genes affected

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

ENSG00000291131 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
NDUFV2P1		n.53224029A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NDUFV2P1	ENST00000596415.1	n.851T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000291131	ENST00000795206.1	n.480+18949A>G		intron_variant	Intron 4 of 4

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

African (AFR) AF: 0.184 AC: 6128 AN: 33258

American (AMR) AF: 0.359 AC: 16044 AN: 44708

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 11457 AN: 26008

East Asian (EAS) AF: 0.747 AC: 29566 AN: 39594

South Asian (SAS) AF: 0.492 AC: 42232 AN: 85862

European-Finnish (FIN) AF: 0.297 AC: 15868 AN: 53414

Middle Eastern (MID) AF: 0.350 AC: 2010 AN: 5744

European-Non Finnish (NFE) AF: 0.367 AC: 402777 AN: 1097498

Other (OTH) AF: 0.384 AC: 23016 AN: 59868

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

African (AFR) AF: 0.195 AC: 8084 AN: 41498

American (AMR) AF: 0.351 AC: 5363 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1510 AN: 3470

East Asian (EAS) AF: 0.735 AC: 3798 AN: 5168

South Asian (SAS) AF: 0.519 AC: 2492 AN: 4806

European-Finnish (FIN) AF: 0.288 AC: 3040 AN: 10560

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24744 AN: 67952

Other (OTH) AF: 0.323 AC: 682 AN: 2114

Alfa AF: 0.360 Hom.: 3903

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
PhyloP100		4.8

Splicing

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

Other links and lift over

dbSNP: rs11084227; hg19: chr19-53727282;