rs10033854

Variant names:

• chr4-69654186-G-A
• rs10033854

Your query was ambiguous. Multiple possible variants found:

• chr4-69654186-G-A
• chr4-69654186-G-C

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 0.479 in 151,810 control chromosomes in the GnomAD database, including 17,629 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 0.48 (17629 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0620
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72610 AN: 151692 Hom.: 17622 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.442

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.621

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.475

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.479 AC: 72651 AN: 151810 Hom.: 17629 Cov.: 32 AF XY: 0.475 AC XY: 35207 AN XY: 74184

African (AFR) AF: 0.501 AC: 20759 AN: 41402

American (AMR) AF: 0.441 AC: 6731 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1646 AN: 3466

East Asian (EAS) AF: 0.621 AC: 3206 AN: 5162

South Asian (SAS) AF: 0.470 AC: 2263 AN: 4816

European-Finnish (FIN) AF: 0.384 AC: 4030 AN: 10506

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.475 AC: 32274 AN: 67884

Other (OTH) AF: 0.499 AC: 1052 AN: 2108

Alfa AF: 0.477 Hom.: 67392

Bravo AF: 0.482

Asia WGS AF: 0.598 AC: 2078 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.31
PhyloP100		-0.062

Splicing

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

Other links and lift over

dbSNP: rs10033854; hg19: chr4-70519904;