rs4144700

Variant names:

• chr11-49349282-C-A
• rs4144700

Your query was ambiguous. Multiple possible variants found:

• chr11-49349282-C-A
• chr11-49349282-C-G

Variant summary

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

The variant allele was found at a frequency of 0.497 in 151,968 control chromosomes in the GnomAD database, including 21,009 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 0.50 (21009 hom., cov: 32)
• Consequence: NOX4P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

Genes affected

NOX4P1 (HGNC:56735): (NOX4 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOX4P1		n.49349282C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255532	ENST00000529674.1	n.478-1916C>A		intron_variant	Intron 3 of 7	6

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75560 AN: 151852 Hom.: 20997 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.717

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.557

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.497 AC: 75578 AN: 151968 Hom.: 21009 Cov.: 32 AF XY: 0.499 AC XY: 37070 AN XY: 74268

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.717

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.579

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.562

Alfa AF: 0.553 Hom.: 4619

Bravo AF: 0.492

Asia WGS AF: 0.495 AC: 1721 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4144700; hg19: chr11-49370834;