chr5-35880718-C-T

Variant names:

• chr5-35880718-C-T
• rs10058453

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 0.702 in 152,132 control chromosomes in the GnomAD database, including 38,501 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 0.70 (38501 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.845 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: 0.702 AC: 106734 AN: 152014 Hom.: 38491 Cov.: 33

Gnomad AFR AF: 0.853

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.573

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.737

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.702 AC: 106787 AN: 152132 Hom.: 38501 Cov.: 33 AF XY: 0.697 AC XY: 51823 AN XY: 74358

African (AFR) AF: 0.852 AC: 35405 AN: 41534

American (AMR) AF: 0.572 AC: 8747 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2214 AN: 3470

East Asian (EAS) AF: 0.420 AC: 2166 AN: 5160

South Asian (SAS) AF: 0.512 AC: 2467 AN: 4818

European-Finnish (FIN) AF: 0.737 AC: 7779 AN: 10562

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45683 AN: 67982

Other (OTH) AF: 0.670 AC: 1415 AN: 2112

Alfa AF: 0.680 Hom.: 50365

Bravo AF: 0.700

Asia WGS AF: 0.536 AC: 1865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.7
DANN	Benign	0.15
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs10058453; hg19: chr5-35880820;