rs1836882

Positions:

• chr11-89498993-T-C

Variant summary

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

The ENST00000532005.1(H3P34):​n.206A>G variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.156 in 153,752 control chromosomes in the GnomAD database, including 2,097 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 0.16 (2079 hom., cov: 32)
  • Exomes 𝑓: 0.11 (18 hom.)
• Consequence: H3P34 ENST00000532005.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.73

Genes affected

H3P34 (HGNC:54467): (H3 histone pseudogene 34)

NOX4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NOX4	NM_001143837.2	c.-305-806A>G		intron_variant			NP_001137309.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
H3P34	ENST00000532005.1	n.206A>G		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.157 AC: 23808 AN: 152016 Hom.: 2067 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.164

GnomAD4 exome AF: 0.113 AC: 183 AN: 1620 Hom.: 18 Cov.: 0 AF XY: 0.109 AC XY: 87 AN XY: 798

Gnomad4 AMR exome AF: 0.375

Gnomad4 ASJ exome AF: 0.125

Gnomad4 EAS exome AF: 0.167

Gnomad4 SAS exome AF: 0.189

Gnomad4 FIN exome AF: 0.101

Gnomad4 NFE exome AF: 0.229

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.157 AC: 23849 AN: 152132 Hom.: 2079 Cov.: 32 AF XY: 0.156 AC XY: 11579 AN XY: 74360

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.126

Gnomad4 OTH AF: 0.171

Alfa AF: 0.131 Hom.: 1819

Bravo AF: 0.163

Asia WGS AF: 0.222 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	4.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1836882; hg19: chr11-89232161; COSMIC: COSV73266391;