5-45252398-A-G

Variant names:

• chr5-45252398-A-G
• rs10035564

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 0.455 in 151,996 control chromosomes in the GnomAD database, including 17,395 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 0.45 (17395 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.119
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 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: 0.455 AC: 69041 AN: 151880 Hom.: 17345 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.455 AC: 69156 AN: 151996 Hom.: 17395 Cov.: 32 AF XY: 0.458 AC XY: 34048 AN XY: 74278

African (AFR) AF: 0.680 AC: 28216 AN: 41474

American (AMR) AF: 0.439 AC: 6691 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1562 AN: 3470

East Asian (EAS) AF: 0.491 AC: 2529 AN: 5152

South Asian (SAS) AF: 0.472 AC: 2276 AN: 4824

European-Finnish (FIN) AF: 0.330 AC: 3485 AN: 10548

Middle Eastern (MID) AF: 0.435 AC: 127 AN: 292

European-Non Finnish (NFE) AF: 0.339 AC: 23071 AN: 67958

Other (OTH) AF: 0.430 AC: 907 AN: 2110

Alfa AF: 0.391 Hom.: 4075

Bravo AF: 0.471

Asia WGS AF: 0.525 AC: 1822 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.8
DANN	Benign	0.56
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10035564; hg19: chr5-45252500;