rs5755703

Variant names:

• chr22-35358420-C-A
• rs5755703

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 0.608 in 151,926 control chromosomes in the GnomAD database, including 31,016 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 0.61 (31016 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.210
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92276 AN: 151808 Hom.: 30944 Cov.: 30

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.503

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.569

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

GnomAD4 genome AF: 0.608 AC: 92414 AN: 151926 Hom.: 31016 Cov.: 30 AF XY: 0.609 AC XY: 45209 AN XY: 74232

African (AFR) AF: 0.896 AC: 37135 AN: 41436

American (AMR) AF: 0.641 AC: 9785 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1373 AN: 3466

East Asian (EAS) AF: 0.735 AC: 3796 AN: 5168

South Asian (SAS) AF: 0.504 AC: 2421 AN: 4806

European-Finnish (FIN) AF: 0.476 AC: 5012 AN: 10524

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31067 AN: 67954

Other (OTH) AF: 0.569 AC: 1201 AN: 2110

Alfa AF: 0.507 Hom.: 63429

Bravo AF: 0.635

Asia WGS AF: 0.603 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.079
DANN	Benign	0.63
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs5755703; hg19: chr22-35754413;