rs653734

Variant names:

• chr1-218847270-A-C
• rs653734

Your query was ambiguous. Multiple possible variants found:

• chr1-218847270-A-C
• chr1-218847270-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.383 in 151,954 control chromosomes in the GnomAD database, including 12,136 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 0.38 (12136 hom., cov: 31)
• Consequence: NXNP1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0790
• Publications: 4 publications found

Genes affected

NXNP1 (HGNC:50561): (nucleoredoxin pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58162 AN: 151836 Hom.: 12144 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.383 AC: 58153 AN: 151954 Hom.: 12136 Cov.: 31 AF XY: 0.381 AC XY: 28283 AN XY: 74242

African (AFR) AF: 0.215 AC: 8901 AN: 41456

American (AMR) AF: 0.429 AC: 6546 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1364 AN: 3466

East Asian (EAS) AF: 0.335 AC: 1728 AN: 5154

South Asian (SAS) AF: 0.249 AC: 1200 AN: 4824

European-Finnish (FIN) AF: 0.469 AC: 4939 AN: 10540

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.473 AC: 32122 AN: 67952

Other (OTH) AF: 0.398 AC: 841 AN: 2112

Alfa AF: 0.338 Hom.: 1401

Bravo AF: 0.378

Asia WGS AF: 0.248 AC: 866 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.71
DANN	Benign	0.73
PhyloP100		-0.079

Splicing

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

Other links and lift over

dbSNP: rs653734; hg19: chr1-219020612;